From 3354f68385e4d94ec3c04b1c51f40e818e21c8dc Mon Sep 17 00:00:00 2001
From: Philip ABBET <philip.abbet@idiap.ch>
Date: Mon, 13 Nov 2017 15:30:32 +0100
Subject: [PATCH] Remove biowave/2, only keep an updated biowave/1 (was never
used before)
---
advanced/databases/biowave/1.json | 335 ++--
advanced/databases/biowave/1.py | 1054 +++++++-----
advanced/databases/biowave/1.rst | 4 +-
advanced/databases/biowave/2.json | 1502 -----------------
advanced/databases/biowave/2.py | 745 --------
advanced/databases/biowave/2.rst | 208 ---
.../array_1d_coordinates/1.json | 7 +
7 files changed, 746 insertions(+), 3109 deletions(-)
delete mode 100644 advanced/databases/biowave/2.json
delete mode 100644 advanced/databases/biowave/2.py
delete mode 100644 advanced/databases/biowave/2.rst
create mode 100644 system/dataformats/system_username/array_1d_coordinates/1.json
diff --git a/advanced/databases/biowave/1.json b/advanced/databases/biowave/1.json
index c5f97c9..e50328a 100644
--- a/advanced/databases/biowave/1.json
+++ b/advanced/databases/biowave/1.json
@@ -15,8 +15,7 @@
"template": "train",
"parameters": {
"protocol": "Idiap_1_1_R_BEAT_test",
- "group": "world",
- "annotated_images": "False"
+ "group": "world"
},
"name": "train"
},
@@ -31,8 +30,7 @@
"parameters": {
"protocol": "Idiap_1_1_R_BEAT_test",
"group": "dev",
- "purpose": "enroll",
- "annotated_images": "False"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -46,8 +44,7 @@
"parameters": {
"protocol": "Idiap_1_1_R_BEAT_test",
"group": "dev",
- "purpose": "probe",
- "annotated_images": "False"
+ "purpose": "probe"
},
"template": "probe"
},
@@ -62,8 +59,7 @@
"parameters": {
"protocol": "Idiap_1_1_R_BEAT_test",
"group": "eval",
- "purpose": "enroll",
- "annotated_images": "False"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -77,8 +73,7 @@
"parameters": {
"protocol": "Idiap_1_1_R_BEAT_test",
"group": "eval",
- "purpose": "probe",
- "annotated_images": "False"
+ "purpose": "probe"
},
"template": "probe"
}
@@ -97,8 +92,7 @@
"template": "train",
"parameters": {
"protocol": "Idiap_5_5_R_BEAT_test",
- "group": "world",
- "annotated_images": "False"
+ "group": "world"
},
"name": "train"
},
@@ -113,8 +107,7 @@
"parameters": {
"protocol": "Idiap_5_5_R_BEAT_test",
"group": "dev",
- "purpose": "enroll",
- "annotated_images": "False"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -128,8 +121,7 @@
"parameters": {
"protocol": "Idiap_5_5_R_BEAT_test",
"group": "dev",
- "purpose": "probe",
- "annotated_images": "False"
+ "purpose": "probe"
},
"template": "probe"
},
@@ -144,8 +136,7 @@
"parameters": {
"protocol": "Idiap_5_5_R_BEAT_test",
"group": "eval",
- "purpose": "enroll",
- "annotated_images": "False"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -159,8 +150,7 @@
"parameters": {
"protocol": "Idiap_5_5_R_BEAT_test",
"group": "eval",
- "purpose": "probe",
- "annotated_images": "False"
+ "purpose": "probe"
},
"template": "probe"
}
@@ -179,8 +169,7 @@
"template": "train",
"parameters": {
"protocol": "Idiap_1_5_R_BEAT_test",
- "group": "world",
- "annotated_images": "False"
+ "group": "world"
},
"name": "train"
},
@@ -195,8 +184,7 @@
"parameters": {
"protocol": "Idiap_1_5_R_BEAT_test",
"group": "dev",
- "purpose": "enroll",
- "annotated_images": "False"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -210,8 +198,7 @@
"parameters": {
"protocol": "Idiap_1_5_R_BEAT_test",
"group": "dev",
- "purpose": "probe",
- "annotated_images": "False"
+ "purpose": "probe"
},
"template": "probe"
},
@@ -226,8 +213,7 @@
"parameters": {
"protocol": "Idiap_1_5_R_BEAT_test",
"group": "eval",
- "purpose": "enroll",
- "annotated_images": "False"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -241,8 +227,7 @@
"parameters": {
"protocol": "Idiap_1_5_R_BEAT_test",
"group": "eval",
- "purpose": "probe",
- "annotated_images": "False"
+ "purpose": "probe"
},
"template": "probe"
}
@@ -261,8 +246,7 @@
"template": "train",
"parameters": {
"protocol": "Idiap_1_1_R",
- "group": "world",
- "annotated_images": "False"
+ "group": "world"
},
"name": "train"
},
@@ -277,8 +261,7 @@
"parameters": {
"protocol": "Idiap_1_1_R",
"group": "dev",
- "purpose": "enroll",
- "annotated_images": "False"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -292,8 +275,7 @@
"parameters": {
"protocol": "Idiap_1_1_R",
"group": "dev",
- "purpose": "probe",
- "annotated_images": "False"
+ "purpose": "probe"
},
"template": "probe"
},
@@ -308,8 +290,7 @@
"parameters": {
"protocol": "Idiap_1_1_R",
"group": "eval",
- "purpose": "enroll",
- "annotated_images": "False"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -323,8 +304,7 @@
"parameters": {
"protocol": "Idiap_1_1_R",
"group": "eval",
- "purpose": "probe",
- "annotated_images": "False"
+ "purpose": "probe"
},
"template": "probe"
}
@@ -343,8 +323,7 @@
"template": "train",
"parameters": {
"protocol": "Idiap_1_5_R",
- "group": "world",
- "annotated_images": "False"
+ "group": "world"
},
"name": "train"
},
@@ -359,8 +338,7 @@
"parameters": {
"protocol": "Idiap_1_5_R",
"group": "dev",
- "purpose": "enroll",
- "annotated_images": "False"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -374,8 +352,7 @@
"parameters": {
"protocol": "Idiap_1_5_R",
"group": "dev",
- "purpose": "probe",
- "annotated_images": "False"
+ "purpose": "probe"
},
"template": "probe"
},
@@ -390,8 +367,7 @@
"parameters": {
"protocol": "Idiap_1_5_R",
"group": "eval",
- "purpose": "enroll",
- "annotated_images": "False"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -405,8 +381,7 @@
"parameters": {
"protocol": "Idiap_1_5_R",
"group": "eval",
- "purpose": "probe",
- "annotated_images": "False"
+ "purpose": "probe"
},
"template": "probe"
}
@@ -425,8 +400,7 @@
"template": "train",
"parameters": {
"protocol": "Idiap_5_5_R",
- "group": "world",
- "annotated_images": "False"
+ "group": "world"
},
"name": "train"
},
@@ -441,8 +415,7 @@
"parameters": {
"protocol": "Idiap_5_5_R",
"group": "dev",
- "purpose": "enroll",
- "annotated_images": "False"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -456,8 +429,7 @@
"parameters": {
"protocol": "Idiap_5_5_R",
"group": "dev",
- "purpose": "probe",
- "annotated_images": "False"
+ "purpose": "probe"
},
"template": "probe"
},
@@ -472,8 +444,7 @@
"parameters": {
"protocol": "Idiap_5_5_R",
"group": "eval",
- "purpose": "enroll",
- "annotated_images": "False"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -487,8 +458,7 @@
"parameters": {
"protocol": "Idiap_5_5_R",
"group": "eval",
- "purpose": "probe",
- "annotated_images": "False"
+ "purpose": "probe"
},
"template": "probe"
}
@@ -507,8 +477,7 @@
"template": "train",
"parameters": {
"protocol": "Idiap_1_1_L",
- "group": "world",
- "annotated_images": "False"
+ "group": "world"
},
"name": "train"
},
@@ -523,8 +492,7 @@
"parameters": {
"protocol": "Idiap_1_1_L",
"group": "dev",
- "purpose": "enroll",
- "annotated_images": "False"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -538,8 +506,7 @@
"parameters": {
"protocol": "Idiap_1_1_L",
"group": "dev",
- "purpose": "probe",
- "annotated_images": "False"
+ "purpose": "probe"
},
"template": "probe"
},
@@ -554,8 +521,7 @@
"parameters": {
"protocol": "Idiap_1_1_L",
"group": "eval",
- "purpose": "enroll",
- "annotated_images": "False"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -569,8 +535,7 @@
"parameters": {
"protocol": "Idiap_1_1_L",
"group": "eval",
- "purpose": "probe",
- "annotated_images": "False"
+ "purpose": "probe"
},
"template": "probe"
}
@@ -589,8 +554,7 @@
"template": "train",
"parameters": {
"protocol": "Idiap_1_5_L",
- "group": "world",
- "annotated_images": "False"
+ "group": "world"
},
"name": "train"
},
@@ -605,8 +569,7 @@
"parameters": {
"protocol": "Idiap_1_5_L",
"group": "dev",
- "purpose": "enroll",
- "annotated_images": "False"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -620,8 +583,7 @@
"parameters": {
"protocol": "Idiap_1_5_L",
"group": "dev",
- "purpose": "probe",
- "annotated_images": "False"
+ "purpose": "probe"
},
"template": "probe"
},
@@ -636,8 +598,7 @@
"parameters": {
"protocol": "Idiap_1_5_L",
"group": "eval",
- "purpose": "enroll",
- "annotated_images": "False"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -651,8 +612,7 @@
"parameters": {
"protocol": "Idiap_1_5_L",
"group": "eval",
- "purpose": "probe",
- "annotated_images": "False"
+ "purpose": "probe"
},
"template": "probe"
}
@@ -671,8 +631,7 @@
"template": "train",
"parameters": {
"protocol": "Idiap_5_5_L",
- "group": "world",
- "annotated_images": "False"
+ "group": "world"
},
"name": "train"
},
@@ -687,8 +646,7 @@
"parameters": {
"protocol": "Idiap_5_5_L",
"group": "dev",
- "purpose": "enroll",
- "annotated_images": "False"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -702,8 +660,7 @@
"parameters": {
"protocol": "Idiap_5_5_L",
"group": "dev",
- "purpose": "probe",
- "annotated_images": "False"
+ "purpose": "probe"
},
"template": "probe"
},
@@ -718,8 +675,7 @@
"parameters": {
"protocol": "Idiap_5_5_L",
"group": "eval",
- "purpose": "enroll",
- "annotated_images": "False"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -733,8 +689,7 @@
"parameters": {
"protocol": "Idiap_5_5_L",
"group": "eval",
- "purpose": "probe",
- "annotated_images": "False"
+ "purpose": "probe"
},
"template": "probe"
}
@@ -753,8 +708,7 @@
"template": "train",
"parameters": {
"protocol": "Idiap_1_1_R_less",
- "group": "world",
- "annotated_images": "False"
+ "group": "world"
},
"name": "train"
},
@@ -769,8 +723,7 @@
"parameters": {
"protocol": "Idiap_1_1_R_less",
"group": "dev",
- "purpose": "enroll",
- "annotated_images": "False"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -784,8 +737,7 @@
"parameters": {
"protocol": "Idiap_1_1_R_less",
"group": "dev",
- "purpose": "probe",
- "annotated_images": "False"
+ "purpose": "probe"
},
"template": "probe"
},
@@ -800,8 +752,7 @@
"parameters": {
"protocol": "Idiap_1_1_R_less",
"group": "eval",
- "purpose": "enroll",
- "annotated_images": "False"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -815,8 +766,7 @@
"parameters": {
"protocol": "Idiap_1_1_R_less",
"group": "eval",
- "purpose": "probe",
- "annotated_images": "False"
+ "purpose": "probe"
},
"template": "probe"
}
@@ -835,8 +785,7 @@
"template": "train",
"parameters": {
"protocol": "Idiap_1_5_R_less",
- "group": "world",
- "annotated_images": "False"
+ "group": "world"
},
"name": "train"
},
@@ -851,8 +800,7 @@
"parameters": {
"protocol": "Idiap_1_5_R_less",
"group": "dev",
- "purpose": "enroll",
- "annotated_images": "False"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -866,8 +814,7 @@
"parameters": {
"protocol": "Idiap_1_5_R_less",
"group": "dev",
- "purpose": "probe",
- "annotated_images": "False"
+ "purpose": "probe"
},
"template": "probe"
},
@@ -882,8 +829,7 @@
"parameters": {
"protocol": "Idiap_1_5_R_less",
"group": "eval",
- "purpose": "enroll",
- "annotated_images": "False"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -897,8 +843,7 @@
"parameters": {
"protocol": "Idiap_1_5_R_less",
"group": "eval",
- "purpose": "probe",
- "annotated_images": "False"
+ "purpose": "probe"
},
"template": "probe"
}
@@ -917,8 +862,7 @@
"template": "train",
"parameters": {
"protocol": "Idiap_5_5_R_less",
- "group": "world",
- "annotated_images": "False"
+ "group": "world"
},
"name": "train"
},
@@ -933,8 +877,7 @@
"parameters": {
"protocol": "Idiap_5_5_R_less",
"group": "dev",
- "purpose": "enroll",
- "annotated_images": "False"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -948,8 +891,7 @@
"parameters": {
"protocol": "Idiap_5_5_R_less",
"group": "dev",
- "purpose": "probe",
- "annotated_images": "False"
+ "purpose": "probe"
},
"template": "probe"
},
@@ -964,8 +906,7 @@
"parameters": {
"protocol": "Idiap_5_5_R_less",
"group": "eval",
- "purpose": "enroll",
- "annotated_images": "False"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -979,8 +920,7 @@
"parameters": {
"protocol": "Idiap_5_5_R_less",
"group": "eval",
- "purpose": "probe",
- "annotated_images": "False"
+ "purpose": "probe"
},
"template": "probe"
}
@@ -995,15 +935,14 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "ViewAnnotations",
"template": "train",
"parameters": {
"protocol": "Idiap_1_1_R_BEAT_test",
- "group": "world",
- "annotated_images": "True"
+ "group": "world"
},
"name": "train"
},
@@ -1013,7 +952,7 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "TemplateViewAnnotations",
@@ -1021,8 +960,7 @@
"parameters": {
"protocol": "Idiap_1_1_R_BEAT_test",
"group": "dev",
- "purpose": "enroll",
- "annotated_images": "True"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -1031,7 +969,7 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "ViewAnnotations",
@@ -1039,8 +977,7 @@
"parameters": {
"protocol": "Idiap_1_1_R_BEAT_test",
"group": "dev",
- "purpose": "probe",
- "annotated_images": "True"
+ "purpose": "probe"
},
"template": "probe"
},
@@ -1050,7 +987,7 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "TemplateViewAnnotations",
@@ -1058,8 +995,7 @@
"parameters": {
"protocol": "Idiap_1_1_R_BEAT_test",
"group": "eval",
- "purpose": "enroll",
- "annotated_images": "True"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -1068,7 +1004,7 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "TemplateViewAnnotations",
@@ -1076,8 +1012,7 @@
"parameters": {
"protocol": "Idiap_1_1_R_BEAT_test",
"group": "eval",
- "purpose": "probe",
- "annotated_images": "True"
+ "purpose": "probe"
},
"template": "probe"
}
@@ -1092,15 +1027,14 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "ViewAnnotations",
"template": "train",
"parameters": {
"protocol": "Idiap_5_5_R_BEAT_test",
- "group": "world",
- "annotated_images": "True"
+ "group": "world"
},
"name": "train"
},
@@ -1110,7 +1044,7 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "TemplateViewAnnotations",
@@ -1118,8 +1052,7 @@
"parameters": {
"protocol": "Idiap_5_5_R_BEAT_test",
"group": "dev",
- "purpose": "enroll",
- "annotated_images": "True"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -1128,7 +1061,7 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "ViewAnnotations",
@@ -1136,8 +1069,7 @@
"parameters": {
"protocol": "Idiap_5_5_R_BEAT_test",
"group": "dev",
- "purpose": "probe",
- "annotated_images": "True"
+ "purpose": "probe"
},
"template": "probe"
},
@@ -1147,7 +1079,7 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "TemplateViewAnnotations",
@@ -1155,8 +1087,7 @@
"parameters": {
"protocol": "Idiap_5_5_R_BEAT_test",
"group": "eval",
- "purpose": "enroll",
- "annotated_images": "True"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -1165,7 +1096,7 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "TemplateViewAnnotations",
@@ -1173,8 +1104,7 @@
"parameters": {
"protocol": "Idiap_5_5_R_BEAT_test",
"group": "eval",
- "purpose": "probe",
- "annotated_images": "True"
+ "purpose": "probe"
},
"template": "probe"
}
@@ -1189,15 +1119,14 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "ViewAnnotations",
"template": "train",
"parameters": {
"protocol": "Idiap_1_1_R",
- "group": "world",
- "annotated_images": "True"
+ "group": "world"
},
"name": "train"
},
@@ -1207,7 +1136,7 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "TemplateViewAnnotations",
@@ -1215,8 +1144,7 @@
"parameters": {
"protocol": "Idiap_1_1_R",
"group": "dev",
- "purpose": "enroll",
- "annotated_images": "True"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -1225,7 +1153,7 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "ViewAnnotations",
@@ -1233,8 +1161,7 @@
"parameters": {
"protocol": "Idiap_1_1_R",
"group": "dev",
- "purpose": "probe",
- "annotated_images": "True"
+ "purpose": "probe"
},
"template": "probe"
},
@@ -1244,7 +1171,7 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "TemplateViewAnnotations",
@@ -1252,8 +1179,7 @@
"parameters": {
"protocol": "Idiap_1_1_R",
"group": "eval",
- "purpose": "enroll",
- "annotated_images": "True"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -1262,7 +1188,7 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "TemplateViewAnnotations",
@@ -1270,8 +1196,7 @@
"parameters": {
"protocol": "Idiap_1_1_R",
"group": "eval",
- "purpose": "probe",
- "annotated_images": "True"
+ "purpose": "probe"
},
"template": "probe"
}
@@ -1286,15 +1211,14 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "ViewAnnotations",
"template": "train",
"parameters": {
"protocol": "Idiap_5_5_R",
- "group": "world",
- "annotated_images": "True"
+ "group": "world"
},
"name": "train"
},
@@ -1304,7 +1228,7 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "TemplateViewAnnotations",
@@ -1312,8 +1236,7 @@
"parameters": {
"protocol": "Idiap_5_5_R",
"group": "dev",
- "purpose": "enroll",
- "annotated_images": "True"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -1322,7 +1245,7 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "ViewAnnotations",
@@ -1330,8 +1253,7 @@
"parameters": {
"protocol": "Idiap_5_5_R",
"group": "dev",
- "purpose": "probe",
- "annotated_images": "True"
+ "purpose": "probe"
},
"template": "probe"
},
@@ -1341,7 +1263,7 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "TemplateViewAnnotations",
@@ -1349,8 +1271,7 @@
"parameters": {
"protocol": "Idiap_5_5_R",
"group": "eval",
- "purpose": "enroll",
- "annotated_images": "True"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -1359,7 +1280,7 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "TemplateViewAnnotations",
@@ -1367,8 +1288,7 @@
"parameters": {
"protocol": "Idiap_5_5_R",
"group": "eval",
- "purpose": "probe",
- "annotated_images": "True"
+ "purpose": "probe"
},
"template": "probe"
}
@@ -1383,15 +1303,14 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "ViewAnnotations",
"template": "train",
"parameters": {
"protocol": "Idiap_1_1_L",
- "group": "world",
- "annotated_images": "True"
+ "group": "world"
},
"name": "train"
},
@@ -1401,7 +1320,7 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "TemplateViewAnnotations",
@@ -1409,8 +1328,7 @@
"parameters": {
"protocol": "Idiap_1_1_L",
"group": "dev",
- "purpose": "enroll",
- "annotated_images": "True"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -1419,7 +1337,7 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "ViewAnnotations",
@@ -1427,8 +1345,7 @@
"parameters": {
"protocol": "Idiap_1_1_L",
"group": "dev",
- "purpose": "probe",
- "annotated_images": "True"
+ "purpose": "probe"
},
"template": "probe"
},
@@ -1438,7 +1355,7 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "TemplateViewAnnotations",
@@ -1446,8 +1363,7 @@
"parameters": {
"protocol": "Idiap_1_1_L",
"group": "eval",
- "purpose": "enroll",
- "annotated_images": "True"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -1456,7 +1372,7 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "TemplateViewAnnotations",
@@ -1464,8 +1380,7 @@
"parameters": {
"protocol": "Idiap_1_1_L",
"group": "eval",
- "purpose": "probe",
- "annotated_images": "True"
+ "purpose": "probe"
},
"template": "probe"
}
@@ -1480,15 +1395,14 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "ViewAnnotations",
"template": "train",
"parameters": {
"protocol": "Idiap_5_5_L",
- "group": "world",
- "annotated_images": "True"
+ "group": "world"
},
"name": "train"
},
@@ -1498,7 +1412,7 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "TemplateViewAnnotations",
@@ -1506,8 +1420,7 @@
"parameters": {
"protocol": "Idiap_5_5_L",
"group": "dev",
- "purpose": "enroll",
- "annotated_images": "True"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -1516,7 +1429,7 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "ViewAnnotations",
@@ -1524,8 +1437,7 @@
"parameters": {
"protocol": "Idiap_5_5_L",
"group": "dev",
- "purpose": "probe",
- "annotated_images": "True"
+ "purpose": "probe"
},
"template": "probe"
},
@@ -1535,7 +1447,7 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "TemplateViewAnnotations",
@@ -1543,8 +1455,7 @@
"parameters": {
"protocol": "Idiap_5_5_L",
"group": "eval",
- "purpose": "enroll",
- "annotated_images": "True"
+ "purpose": "enroll"
},
"template": "enroll"
},
@@ -1553,7 +1464,7 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1",
"client_id": "{{ system_user.username }}/uint64/1"
},
"view": "TemplateViewAnnotations",
@@ -1561,8 +1472,7 @@
"parameters": {
"protocol": "Idiap_5_5_L",
"group": "eval",
- "purpose": "probe",
- "annotated_images": "True"
+ "purpose": "probe"
},
"template": "probe"
}
@@ -1577,13 +1487,12 @@
"image": "{{ system_user.username }}/array_2d_uint8/1",
"vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
"ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1"
+ "alignment_annotations": "{{ system_user.username }}/array_1d_coordinates/1"
},
"view": "AnnotationBenchmark",
"template": "annotation_benchmark",
"parameters": {
- "protocol": "Idiap_1_1_R",
- "annotated_images": "True"
+ "protocol": "Idiap_1_1_R"
},
"name": "annotations"
}
diff --git a/advanced/databases/biowave/1.py b/advanced/databases/biowave/1.py
index 934a0f1..cad66fd 100644
--- a/advanced/databases/biowave/1.py
+++ b/advanced/databases/biowave/1.py
@@ -1,569 +1,745 @@
-import os.path
+###############################################################################
+# #
+# Copyright (c) 2017 Idiap Research Institute, http://www.idiap.ch/ #
+# Contact: beat.support@idiap.ch #
+# #
+# This file is part of the beat.examples module of the BEAT platform. #
+# #
+# Commercial License Usage #
+# Licensees holding valid commercial BEAT licenses may use this file in #
+# accordance with the terms contained in a written agreement between you #
+# and Idiap. For further information contact tto@idiap.ch #
+# #
+# Alternatively, this file may be used under the terms of the GNU Affero #
+# Public License version 3 as published by the Free Software and appearing #
+# in the file LICENSE.AGPL included in the packaging of this file. #
+# The BEAT platform is distributed in the hope that it will be useful, but #
+# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY #
+# or FITNESS FOR A PARTICULAR PURPOSE. #
+# #
+# You should have received a copy of the GNU Affero Public License along #
+# with the BEAT platform. If not, see http://www.gnu.org/licenses/. #
+# #
+###############################################################################
+
+import os
import numpy as np
import bob.io.base
import bob.io.image
import bob.db.biowave_v1
-def str_to_bool(string):
- if string == 'True':
- return True
- elif string == 'False':
- return False
- else:
- raise ValueError
+#----------------------------------------------------------
+
+
+def get_client_end_index(objs, client_id, client_start_index,
+ start_index, end_index):
+ client_end_index = client_start_index
+
+ while client_end_index + 1 <= end_index:
+ obj = objs[client_end_index + 1 - start_index]
+
+ if isinstance(obj, tuple):
+ obj = obj[1]
+
+ if obj.client_id != client_id:
+ return client_end_index
+
+ client_end_index += 1
+
+ return end_index
+
+
+#----------------------------------------------------------
+
+
+def get_model_end_index(objs, model_id, model_start_index,
+ start_index, end_index):
+ model_end_index = model_start_index
+
+ while model_end_index + 1 <= end_index:
+ obj = objs[model_end_index + 1 - start_index]
+
+ if obj.model_id != model_id:
+ return model_end_index
+
+ model_end_index += 1
+
+ return end_index
+
+
+#----------------------------------------------------------
class View:
- def setup(self,
- root_folder,
- outputs,
- parameters,
- force_start_index=None,
- force_end_index=None):
+ """Outputs:
+ - image: "{{ system_user.username }}/array_2d_uint8/1"
+ - client_id: "{{ system_user.username }}/uint64/1"
+
+ Several "image" are associated with a given "client_id".
+
+ --------------- --------------- --------------- --------------- --------------- ---------------
+ | image | | image | | image | | image | | image | | image |
+ --------------- --------------- --------------- --------------- --------------- ---------------
+ ----------------------------------------------- -----------------------------------------------
+ | client_id | | client_id |
+ ----------------------------------------------- -----------------------------------------------
+ """
- self.root_folder = os.path.join(root_folder, '')
- self.outputs = outputs
- self.parameters = parameters
+ def setup(self, root_folder, outputs, parameters, force_start_index=None,
+ force_end_index=None):
- self.parameters['annotated_images'] = \
- str_to_bool(self.parameters.get('annotated_images', False))
+ # Initialisations
+ self.root_folder = root_folder
+ self.outputs = outputs
+ self.parameters = parameters
+ # Open the database and load the objects to provide via the outputs
self.db = bob.db.biowave_v1.Database()
- self.objs = self.db.objects(
- protocol=self.parameters['protocol'],
- purposes=self.parameters.get('purpose', None),
- groups=[self.parameters['group']],
- annotated_images=self.parameters['annotated_images'],
- imagedir=self.root_folder)
-
- self.next_index = 0
-
- self.force_start_index = force_start_index
- self.force_end_index = force_end_index
-
- # Retrieve only 'useful' data
- # End index
- if self.force_end_index is not None:
- self.objs = self.objs[:self.force_end_index+1]
- # Start index
- if self.force_start_index is not None:
- self.objs = self.objs[self.force_start_index:]
- self.next_index = self.force_start_index
- else:
- self.force_start_index = 0
+ self.objs = sorted(self.db.objects(protocol=self.parameters['protocol'],
+ groups=[self.parameters['group']],
+ purposes=self.parameters.get('purpose', None),
+ annotated_images=False,
+ imagedir=self.root_folder),
+ key=lambda x: (x.client_id, x.id))
+
+ # Determine the range of indices that must be provided
+ self.start_index = force_start_index if force_start_index is not None else 0
+ self.end_index = force_end_index if force_end_index is not None else len(self.objs) - 1
+
+ self.objs = self.objs[self.start_index : self.end_index + 1]
+
+ self.next_index = self.start_index
return True
- def done(self):
- return (self.next_index-self.force_start_index >= len(self.objs))
+ def done(self, last_data_index):
+ return last_data_index >= self.end_index
def next(self):
- obj = self.objs[self.next_index-self.force_start_index]
+ obj = self.objs[self.next_index - self.start_index]
- if self.outputs['client_id'].isConnected():
- client_id = obj.get_client_id
- self.outputs['client_id'].write({'value':
- np.uint64(client_id)},
- self.next_index)
+ # Output: client_id (only provide data when the client_id change)
+ if self.outputs['client_id'].isConnected() and \
+ self.outputs['client_id'].last_written_data_index < self.next_index:
- if "enroll" in self.parameters.get('purpose', ""):
- if self.outputs['model_id'].isConnected():
+ client_end_index = get_client_end_index(self.objs, obj.client_id,
+ self.next_index,
+ self.start_index,
+ self.end_index)
- model_id = \
- self.db.file_model_id(file=obj,
- protocol=self.parameters['protocol'])
- model_id = model_id.encode('utf-8')
- self.outputs['model_id'].write({'text':
- model_id},
- self.next_index)
+ self.outputs['client_id'].write(
+ {
+ 'value': np.uint64(obj.client_id)
+ },
+ client_end_index
+ )
+ # Output: image (provide data at each iteration)
if self.outputs['image'].isConnected():
- data = {
- 'value': obj.load(directory=self.root_folder)
- }
-
- self.outputs['image'].write(data, self.next_index)
+ self.outputs['image'].write(
+ {
+ 'value': obj.load(directory=self.root_folder)
+ },
+ self.next_index
+ )
- self.next_index += 1
+ # Determine the next data index that must be provided
+ self.next_index = 1 + min([ x.last_written_data_index for x in self.outputs
+ if x.isConnected() ]
+ )
return True
+
+#----------------------------------------------------------
+
+
class TemplateView:
- # Reasoning: Each client may have a number of models in certain databases.
- # So, each model receives an unique identifier. Those identifiers are
- # linked to the client identifier and contain a number of images to
- # generated the model from.
- def setup(self,
- root_folder,
- outputs,
- parameters,
- force_start_index=None,
+ """Outputs:
+ - image: "{{ system_user.username }}/array_2d_uint8/1"
+ - client_id: "{{ system_user.username }}/uint64/1"
+ - model_id: "{{ system_user.username }}/text/1"
+
+ Several "image" are associated with a given "model_id".
+ Several "model_id" are associated with a given "client_id".
+
+ --------------- --------------- --------------- --------------- --------------- ---------------
+ | image | | image | | image | | image | | image | | image |
+ --------------- --------------- --------------- --------------- --------------- ---------------
+ ----------------------------------------------- -----------------------------------------------
+ | model_id | | model_id |
+ ----------------------------------------------- -----------------------------------------------
+ -----------------------------------------------------------------------------------------------
+ | client_id |
+ -----------------------------------------------------------------------------------------------
+
+ Note: for this particular database, there is only one "image"
+ per "model_id".
+ """
+
+ def setup(self, root_folder, outputs, parameters, force_start_index=None,
force_end_index=None):
- self.root_folder = os.path.join(root_folder, '')
- self.outputs = outputs
- self.parameters = parameters
-
- self.parameters['annotated_images'] = \
- str_to_bool(self.parameters.get('annotated_images', False))
+ # Initialisations
+ self.root_folder = root_folder
+ self.outputs = outputs
+ self.parameters = parameters
+ # Open the database and load the objects to provide via the outputs
self.db = bob.db.biowave_v1.Database()
- self.template_ids = \
- sorted(self.db.model_ids(protocol=self.parameters['protocol'],
- groups=[self.parameters['group']],
- annotated_images=self.parameters['annotated_images'],
- imagedir=self.root_folder))
-
- self.objs = None
- self.current_template_index = 0
- self.current_obj_index = 0
- self.next_index = 0
+ self.objs = sorted(self.db.objects(protocol=self.parameters['protocol'],
+ purposes=self.parameters['purpose'],
+ groups=[self.parameters['group']],
+ annotated_images=False,
+ imagedir=self.root_folder),
+ key=lambda x: (x.client_id, x.model_id, x.id))
- self.force_start_index = force_start_index
- self.force_end_index = force_end_index
+ # Determine the range of indices that must be provided
+ self.start_index = force_start_index if force_start_index is not None else 0
+ self.end_index = force_end_index if force_end_index is not None else len(self.objs) - 1
- # We don't know how many objects we will have, so we can't operate with
- # self.force_end_index.
- if self.force_start_index is None:
- self.force_start_index = 0
+ self.objs = self.objs[self.start_index : self.end_index + 1]
- # Example taxen from atnt/3 - idea to iterate through ``next`` method
- # to get indexes right
- while self.next_index < self.force_start_index:
- self.next()
+ self.next_index = self.start_index
return True
- def done(self):
- # return (self.next_index-self.force_start_index >= len(self.objs))
- return ((self.current_template_index >= len(self.template_ids)) or
- (self.force_end_index is not None and
- self.force_end_index < self.next_index))
+ def done(self, last_data_index):
+ return last_data_index >= self.end_index
def next(self):
- if self.objs is None:
- # probe for the specific objects concerning a given client
- self.objs = \
- sorted(self.db.objects(protocol=self.parameters['protocol'],
- purposes="enroll", # We do this ONLY for templates
- groups=[self.parameters['group']],
- annotated_images=self.parameters['annotated_images'],
- imagedir=self.root_folder,
- model_ids=[self.template_ids[self.current_template_index]]),
- key=lambda x: x.id)
-
- if (self.force_start_index <= self.next_index and
- (self.force_end_index is None or
- self.force_end_index >= self.next_index)):
- if self.outputs['model_id'].isConnected():
- # for this database the
- # ``self.template_ids[self.current_template_index]`` is the
- # ``model_id``:
- model_id = self.template_ids[self.current_template_index]
- model_id = model_id.encode('utf-8')
- self.outputs['model_id'].write({'text':
- model_id},
- self.next_index+len(self.objs)-1)
-
- if self.outputs['client_id'].isConnected():
- client_id = self.objs[0].get_client_id
- self.outputs['client_id'].write({'value':
- np.uint64(client_id)},
- self.next_index+len(self.objs)-1)
-
- obj = self.objs[self.current_obj_index]
-
+ obj = self.objs[self.next_index - self.start_index]
+
+ # Output: model_id (only provide data when the model_id change)
+ if self.outputs['model_id'].isConnected() and \
+ self.outputs['model_id'].last_written_data_index < self.next_index:
+
+ model_end_index = get_model_end_index(self.objs, obj.model_id,
+ self.next_index,
+ self.start_index,
+ self.end_index)
+
+ self.outputs['model_id'].write(
+ {
+ 'text': obj.model_id.encode('utf-8')
+ },
+ model_end_index
+ )
+
+ # Output: client_id (only provide data when the client_id change)
+ if self.outputs['client_id'].isConnected() and \
+ self.outputs['client_id'].last_written_data_index < self.next_index:
+
+ # Please pay attention - we can use the object CLIENT ID as long as we
+ # don't use both hands data of the same client in the same protocol.
+ client_end_index = get_client_end_index(self.objs, obj.client_id,
+ self.next_index,
+ self.start_index,
+ self.end_index)
+
+ self.outputs['client_id'].write(
+ {
+ 'value': np.uint64(obj.client_id)
+ },
+ client_end_index
+ )
+
+ # Output: image (provide data at each iteration)
if self.outputs['image'].isConnected():
- # This line is taken from the "atnt/3" database's view. It seams
- # that this could cause problems, if model has N images, but
- # ``self.force_end_index`` /= N*M, where M -- Natural number:
- if (self.force_start_index <= self.next_index and
- (self.force_end_index is None or
- self.force_end_index >= self.next_index)):
- # No need to test if output is connected:
- # if self.outputs['image'].isConnected():
- data = {
+ self.outputs['image'].write(
+ {
'value': obj.load(directory=self.root_folder)
- }
- self.outputs['image'].write(data, self.next_index)
+ },
+ self.next_index
+ )
- self.next_index += 1
- self.current_obj_index += 1
+ # Determine the next data index that must be provided
+ self.next_index = 1 + min([ x.last_written_data_index for x in self.outputs
+ if x.isConnected() ]
+ )
- else:
- self.next_index += len(self.objs)
- self.current_obj_index = len(self.objs)
+ return True
- if self.current_obj_index == len(self.objs):
- self.objs = None
- self.current_obj_index = 0
- self.current_template_index += 1
- return True
+#----------------------------------------------------------
class ViewAnnotations:
- def setup(self,
- root_folder,
- outputs,
- parameters,
- force_start_index=None,
+ """Outputs:
+ - image: "{{ system_user.username }}/array_2d_uint8/1"
+ - vein_annotations: "{{ system_user.username }}/array_2d_uint8/1"
+ - ROI_annotations: "{{ system_user.username }}/array_2d_uint8/1"
+ - alignment_annotations: "{{ system_user.username }}/array_1d_coordinates/1"
+ - client_id: "{{ system_user.username }}/uint64/1"
+
+ One "vein_annotations" are associated with a given "image".
+ One "ROI_annotations" are associated with a given "image".
+ One "alignment_annotations" are associated with a given "image".
+ Several "image" are associated with a given "client_id".
+
+ ------------------------- ------------------------- ------------------------- -------------------------
+ | image | | image | | image | | image |
+ ------------------------- ------------------------- ------------------------- -------------------------
+ ------------------------- ------------------------- ------------------------- -------------------------
+ | vein_annotations | | vein_annotations | | vein_annotations | | vein_annotations |
+ ------------------------- ------------------------- ------------------------- -------------------------
+ ------------------------- ------------------------- ------------------------- -------------------------
+ | ROI_annotations | | ROI_annotations | | ROI_annotations | | ROI_annotations |
+ ------------------------- ------------------------- ------------------------- -------------------------
+ ------------------------- ------------------------- ------------------------- -------------------------
+ | alignment_annotations | | alignment_annotations | | alignment_annotations | | alignment_annotations |
+ ------------------------- ------------------------- ------------------------- -------------------------
+ --------------------------------------------------- ---------------------------------------------------
+ | client_id | | client_id |
+ --------------------------------------------------- ---------------------------------------------------
+ """
+
+ def setup(self, root_folder, outputs, parameters, force_start_index=None,
force_end_index=None):
- self.root_folder = os.path.join(root_folder, '')
- self.outputs = outputs
- self.parameters = parameters
-
- self.parameters['annotated_images'] = \
- str_to_bool(self.parameters.get('annotated_images', False))
+ # Initialisations
+ self.root_folder = root_folder
+ self.outputs = outputs
+ self.parameters = parameters
+ # Open the database and load the objects to provide via the outputs
self.db = bob.db.biowave_v1.Database()
- self.objs = self.db.objects(
- protocol=self.parameters['protocol'],
- purposes=self.parameters.get('purpose', None),
- groups=[self.parameters['group']],
- annotated_images=self.parameters['annotated_images'],
- imagedir=self.root_folder)
-
- self.next_index = 0
-
- self.force_start_index = force_start_index
- self.force_end_index = force_end_index
-
- # Retrieve only 'useful' data
- # End index
- if self.force_end_index is not None:
- self.objs = self.objs[:self.force_end_index+1]
- # Start index
- if self.force_start_index is not None:
- self.objs = self.objs[self.force_start_index:]
- self.next_index = self.force_start_index
- else:
- self.force_start_index = 0
+
+ self.objs = sorted(self.db.objects(protocol=self.parameters['protocol'],
+ groups=[self.parameters['group']],
+ purposes=self.parameters.get('purpose', None),
+ annotated_images=True,
+ imagedir=self.root_folder),
+ key=lambda x: (x.client_id, x.id))
+
+ # Determine the range of indices that must be provided
+ self.start_index = force_start_index if force_start_index is not None else 0
+ self.end_index = force_end_index if force_end_index is not None else len(self.objs) - 1
+
+ self.objs = self.objs[self.start_index : self.end_index + 1]
+
+ self.next_index = self.start_index
return True
- def done(self):
- return (self.next_index-self.force_start_index >= len(self.objs))
+ def done(self, last_data_index):
+ return last_data_index >= self.end_index
def next(self):
- obj = self.objs[self.next_index-self.force_start_index]
- if self.outputs['client_id'].isConnected():
- client_id = obj.get_client_id
- self.outputs['client_id'].write({'value':
- np.uint64(client_id)},
- self.next_index)
-
- if "enroll" in self.parameters.get('purpose', ""):
- if self.outputs['model_id'].isConnected():
- model_id = \
- self.db.file_model_id(file=obj,
- protocol=self.parameters['protocol'])
- model_id = model_id.encode('utf-8')
- self.outputs['model_id'].write({'text':
- model_id},
- self.next_index)
+ obj = self.objs[self.next_index - self.start_index]
- if self.outputs['image'].isConnected():
- data = {
- 'value': obj.load(directory=self.root_folder)
- }
- self.outputs['image'].write(data, self.next_index)
+ # Output: client_id (only provide data when the client_id change)
+ if self.outputs['client_id'].isConnected() and \
+ self.outputs['client_id'].last_written_data_index < self.next_index:
- if self.outputs['vein_annotations'].isConnected():
- data = {
- 'value': obj.construct_vein_image(directory=self.root_folder)
- }
- self.outputs['vein_annotations'].write(data, self.next_index)
+ client_end_index = get_client_end_index(self.objs, obj.client_id,
+ self.next_index,
+ self.start_index,
+ self.end_index)
- if self.outputs['ROI_annotations'].isConnected():
- data = {
- 'value': obj.construct_ROI_image(directory=self.root_folder)
- }
- self.outputs['ROI_annotations'].write(data, self.next_index)
+ self.outputs['client_id'].write(
+ {
+ 'value': np.uint64(obj.client_id)
+ },
+ client_end_index
+ )
+ # Output: vein_annotations (provide data at each iteration)
+ if self.outputs['vein_annotations'].isConnected():
+ self.outputs['vein_annotations'].write(
+ {
+ 'value': obj.construct_vein_image(directory=self.root_folder)
+ },
+ self.next_index
+ )
+
+ # Output: ROI_annotations (provide data at each iteration)
+ if self.outputs['ROI_annotations'].isConnected():
+ self.outputs['ROI_annotations'].write(
+ {
+ 'value': obj.construct_ROI_image(directory=self.root_folder)
+ },
+ self.next_index
+ )
+
+ # Output: alignment_annotations (provide data at each iteration)
if self.outputs['alignment_annotations'].isConnected():
- alignment_annotations = \
- obj.alignment_annotations(directory=self.root_folder)
+ alignment_annotations = obj.alignment_annotations(directory=self.root_folder)
+
coordinate_list = []
for annotation in alignment_annotations:
coordinate = {
- "y": np.int32(annotation[0]),
- "x": np.int32(annotation[1])
- }
+ "y": np.int32(annotation[0]),
+ "x": np.int32(annotation[1])
+ }
coordinate_list.append(coordinate)
- data = {'coordinate_list': coordinate_list}
- self.outputs['alignment_annotations'].write(data, self.next_index)
+ self.outputs['alignment_annotations'].write(
+ {
+ 'value': coordinate_list
+ },
+ self.next_index
+ )
+
+ # Output: image (provide data at each iteration)
+ if self.outputs['image'].isConnected():
+ self.outputs['image'].write(
+ {
+ 'value': obj.load(directory=self.root_folder)
+ },
+ self.next_index
+ )
+
+ # Determine the next data index that must be provided
+ self.next_index = 1 + min([ x.last_written_data_index for x in self.outputs
+ if x.isConnected() ]
+ )
- self.next_index += 1
return True
+#----------------------------------------------------------
+
class TemplateViewAnnotations:
- # Reasoning: Each client may have a number of models in certain databases.
- # So, each model receives an unique identifier. Those identifiers are
- # linked to the client identifier and contain a number of images to
- # generated the model from.
- def setup(self,
- root_folder,
- outputs,
- parameters,
- force_start_index=None,
+ """Outputs:
+ - image: "{{ system_user.username }}/array_2d_uint8/1"
+ - vein_annotations: "{{ system_user.username }}/array_2d_uint8/1"
+ - ROI_annotations: "{{ system_user.username }}/array_2d_uint8/1"
+ - alignment_annotations: "{{ system_user.username }}/array_1d_coordinates/1"
+ - model_id: "{{ system_user.username }}/model_id/1"
+ - client_id: "{{ system_user.username }}/uint64/1"
+
+ One "vein_annotations" are associated with a given "image".
+ One "ROI_annotations" are associated with a given "image".
+ One "alignment_annotations" are associated with a given "image".
+ Several "image" are associated with a given "model_id".
+ Several "model_id" are associated with a given "client_id".
+
+ ------------------------- ------------------------- ------------------------- -------------------------
+ | image | | image | | image | | image |
+ ------------------------- ------------------------- ------------------------- -------------------------
+ ------------------------- ------------------------- ------------------------- -------------------------
+ | vein_annotations | | vein_annotations | | vein_annotations | | vein_annotations |
+ ------------------------- ------------------------- ------------------------- -------------------------
+ ------------------------- ------------------------- ------------------------- -------------------------
+ | ROI_annotations | | ROI_annotations | | ROI_annotations | | ROI_annotations |
+ ------------------------- ------------------------- ------------------------- -------------------------
+ ------------------------- ------------------------- ------------------------- -------------------------
+ | alignment_annotations | | alignment_annotations | | alignment_annotations | | alignment_annotations |
+ ------------------------- ------------------------- ------------------------- -------------------------
+ --------------------------------------------------- ---------------------------------------------------
+ | model_id | | model_id |
+ --------------------------------------------------- ---------------------------------------------------
+ -------------------------------------------------------------------------------------------------------
+ | client_id |
+ -------------------------------------------------------------------------------------------------------
+
+ Note: for this particular database, there is only one "image"
+ per "model_id".
+ """
+
+ def setup(self, root_folder, outputs, parameters, force_start_index=None,
force_end_index=None):
- self.root_folder = os.path.join(root_folder, '')
- self.outputs = outputs
- self.parameters = parameters
-
- self.parameters['annotated_images'] = \
- str_to_bool(self.parameters.get('annotated_images', False))
+ # Initialisations
+ self.root_folder = root_folder
+ self.outputs = outputs
+ self.parameters = parameters
+ # Open the database and load the objects to provide via the outputs
self.db = bob.db.biowave_v1.Database()
- self.template_ids = \
- sorted(self.db.model_ids(protocol=self.parameters['protocol'],
- groups=[self.parameters['group']],
- annotated_images=self.parameters['annotated_images'],
- imagedir=self.root_folder))
-
- self.objs = None
- self.current_template_index = 0
- self.current_obj_index = 0
- self.next_index = 0
+ self.objs = sorted(self.db.objects(protocol=self.parameters['protocol'],
+ purposes=self.parameters['purpose'],
+ groups=[self.parameters['group']],
+ annotated_images=True,
+ imagedir=self.root_folder),
+ key=lambda x: (x.client_id, x.model_id, x.id))
- self.force_start_index = force_start_index
- self.force_end_index = force_end_index
+ # Determine the range of indices that must be provided
+ self.start_index = force_start_index if force_start_index is not None else 0
+ self.end_index = force_end_index if force_end_index is not None else len(self.objs) - 1
- # We don't know how many objects we will have, so we can't operate with
- # self.force_end_index.
- if self.force_start_index is None:
- self.force_start_index = 0
+ self.objs = self.objs[self.start_index : self.end_index + 1]
- # Example taxen from atnt/3 - idea to iterate through ``next`` method
- # to get indexes right:
- while self.next_index < self.force_start_index:
- self.next()
+ self.next_index = self.start_index
return True
- def done(self):
- # return (self.next_index-self.force_start_index >= len(self.objs))
- return ((self.current_template_index >= len(self.template_ids)) or
- (self.force_end_index is not None and
- self.force_end_index < self.next_index))
+ def done(self, last_data_index):
+ return last_data_index >= self.end_index
def next(self):
- if self.objs is None:
- # probe for the specific objects concerning a given client
- self.objs = \
- sorted(self.db.objects(protocol=self.parameters['protocol'],
- purposes="enroll", # We do this ONLY for templates
- groups=[self.parameters['group']],
- annotated_images=self.parameters['annotated_images'],
- imagedir=self.root_folder,
- model_ids=[self.template_ids[self.current_template_index]]),
- key=lambda x: x.id)
-
- if (self.force_start_index <= self.next_index and
- (self.force_end_index is None or
- self.force_end_index >= self.next_index)):
- if self.outputs['model_id'].isConnected():
- # for this database the
- # ``self.template_ids[self.current_template_index]`` is the
- # ``model_id``:
- model_id = self.template_ids[self.current_template_index]
- model_id = model_id.encode('utf-8')
- self.outputs['model_id'].write({'text':
- model_id},
- self.next_index+len(self.objs)-1)
- if self.outputs['client_id'].isConnected():
- client_id = self.objs[0].get_client_id
- self.outputs['client_id'].write({'value':
- np.uint64(client_id)},
- self.next_index+len(self.objs)-1)
-
- obj = self.objs[self.current_obj_index]
-
- if (self.outputs['image'].isConnected() or
- self.outputs['vein_annotations'].isConnected() or
- self.outputs['ROI_annotations'].isConnected() or
- self.outputs['alignment_annotations'].isConnected()):
-
- # This line is taken from the "atnt/3" database's view. It seams
- # that this could cause problems, if model has N images, but
- # ``self.force_end_index`` /= N*M, where M -- Natural number:
- if (self.force_start_index <= self.next_index and
- (self.force_end_index is None or
- self.force_end_index >= self.next_index)):
-
- if self.outputs['image'].isConnected():
- data = {
- 'value': obj.load(directory=self.root_folder)
- }
- self.outputs['image'].write(data, self.next_index)
-
- if self.outputs['vein_annotations'].isConnected():
- data = {
- 'value': obj.construct_vein_image(directory=self.root_folder)
- }
- self.outputs['vein_annotations'].write(data,
- self.next_index)
-
- if self.outputs['ROI_annotations'].isConnected():
- data = {
- 'value': obj.construct_ROI_image(directory=self.root_folder)
- }
- self.outputs['ROI_annotations'].write(data,
- self.next_index)
-
- if self.outputs['alignment_annotations'].isConnected():
- alignment_annotations = \
- obj.alignment_annotations(directory=self.root_folder)
- coordinate_list = []
- for annotation in alignment_annotations:
- coordinate = {
- "y": np.int32(annotation[0]),
- "x": np.int32(annotation[1])
- }
- coordinate_list.append(coordinate)
- data = {'coordinate_list': coordinate_list}
-
- self.outputs['alignment_annotations'].write(data,
- self.next_index)
-
- self.next_index += 1
- self.current_obj_index += 1
-
- else:
- self.next_index += len(self.objs)
- self.current_obj_index = len(self.objs)
-
- if self.current_obj_index == len(self.objs):
- self.objs = None
- self.current_obj_index = 0
- self.current_template_index += 1
+ obj = self.objs[self.next_index - self.start_index]
+
+ # Output: model_id (only provide data when the model_id change)
+ if self.outputs['model_id'].isConnected() and \
+ self.outputs['model_id'].last_written_data_index < self.next_index:
+
+ model_end_index = get_model_end_index(self.objs, obj.model_id,
+ self.next_index,
+ self.start_index,
+ self.end_index)
+
+ self.outputs['model_id'].write(
+ {
+ 'text': obj.model_id.encode('utf-8')
+ },
+ model_end_index
+ )
+
+ # Output: client_id (only provide data when the client_id change)
+ if self.outputs['client_id'].isConnected() and \
+ self.outputs['client_id'].last_written_data_index < self.next_index:
+
+ # Please pay attention - we can use the object CLIENT ID as long as we
+ # don't use both hands data of the same client in the same protocol.
+ client_end_index = get_client_end_index(self.objs, obj.client_id,
+ self.next_index,
+ self.start_index,
+ self.end_index)
+
+ self.outputs['client_id'].write(
+ {
+ 'value': np.uint64(obj.client_id)
+ },
+ client_end_index
+ )
+
+ # Output: vein_annotations (provide data at each iteration)
+ if self.outputs['vein_annotations'].isConnected():
+ self.outputs['vein_annotations'].write(
+ {
+ 'value': obj.construct_vein_image(directory=self.root_folder)
+ },
+ self.next_index
+ )
+
+ # Output: ROI_annotations (provide data at each iteration)
+ if self.outputs['ROI_annotations'].isConnected():
+ self.outputs['ROI_annotations'].write(
+ {
+ 'value': obj.construct_ROI_image(directory=self.root_folder)
+ },
+ self.next_index
+ )
+
+ # Output: alignment_annotations (provide data at each iteration)
+ if self.outputs['alignment_annotations'].isConnected():
+ alignment_annotations = obj.alignment_annotations(directory=self.root_folder)
+
+ coordinate_list = []
+ for annotation in alignment_annotations:
+ coordinate = {
+ "y": np.int32(annotation[0]),
+ "x": np.int32(annotation[1])
+ }
+ coordinate_list.append(coordinate)
+
+ self.outputs['alignment_annotations'].write(
+ {
+ 'value': coordinate_list
+ },
+ self.next_index
+ )
+
+ # Output: image (provide data at each iteration)
+ if self.outputs['image'].isConnected():
+ self.outputs['image'].write(
+ {
+ 'value': obj.load(directory=self.root_folder)
+ },
+ self.next_index
+ )
+
+ # Determine the next data index that must be provided
+ self.next_index = 1 + min([ x.last_written_data_index for x in self.outputs
+ if x.isConnected() ]
+ )
return True
-class AnnotationBenchmark:
- def setup(self,
- root_folder,
- outputs,
- parameters,
- force_start_index=None,
- force_end_index=None):
+#----------------------------------------------------------
- self.parameters = parameters
- self.parameters['annotated_images'] = \
- str_to_bool(self.parameters.get('annotated_images', False))
+class AnnotationBenchmark:
+ """Outputs:
+ - image: "{{ system_user.username }}/array_2d_uint8/1"
+ - vein_annotations: "{{ system_user.username }}/array_2d_uint8/1"
+ - ROI_annotations: "{{ system_user.username }}/array_2d_uint8/1"
+ - alignment_annotations: "{{ system_user.username }}/array_1d_coordinates/1"
+
+ One "vein_annotations" are associated with a given "image".
+ One "ROI_annotations" are associated with a given "image".
+ One "alignment_annotations" are associated with a given "image".
+
+ ------------------------- ------------------------- ------------------------- -------------------------
+ | image | | image | | image | | image |
+ ------------------------- ------------------------- ------------------------- -------------------------
+ ------------------------- ------------------------- ------------------------- -------------------------
+ | vein_annotations | | vein_annotations | | vein_annotations | | vein_annotations |
+ ------------------------- ------------------------- ------------------------- -------------------------
+ ------------------------- ------------------------- ------------------------- -------------------------
+ | ROI_annotations | | ROI_annotations | | ROI_annotations | | ROI_annotations |
+ ------------------------- ------------------------- ------------------------- -------------------------
+ ------------------------- ------------------------- ------------------------- -------------------------
+ | alignment_annotations | | alignment_annotations | | alignment_annotations | | alignment_annotations |
+ ------------------------- ------------------------- ------------------------- -------------------------
+ """
+
+ def setup(self, root_folder, outputs, parameters, force_start_index=None,
+ force_end_index=None):
- self.root_folder = os.path.join(root_folder, '')
- self.outputs = outputs
+ # Initialisations
+ self.root_folder = root_folder
+ self.outputs = outputs
+ self.parameters = parameters
+ # Open the database and load the objects to provide via the outputs
self.db = bob.db.biowave_v1.Database()
- self.objs = \
- self.db.objects(protocol=self.parameters['protocol'],
- annotated_images=self.parameters['annotated_images'],
- imagedir=self.root_folder)
+ self.objs = sorted(self.db.objects(protocol=self.parameters['protocol'],
+ annotated_images=True,
+ imagedir=self.root_folder),
+ key=lambda x: x.id)
- self.next_index = 0
+ # Determine the range of indices that must be provided
+ self.start_index = force_start_index if force_start_index is not None else 0
+ self.end_index = force_end_index if force_end_index is not None else len(self.objs) - 1
- self.force_start_index = force_start_index
- self.force_end_index = force_end_index
+ self.objs = self.objs[self.start_index : self.end_index + 1]
- # Retrieve only 'useful' data
- # End index
- if self.force_end_index is not None:
- self.objs = self.objs[:self.force_end_index+1]
- # Start index
- if self.force_start_index is not None:
- self.objs = self.objs[self.force_start_index:]
- self.next_index = self.force_start_index
- else:
- self.force_start_index = 0
+ self.next_index = self.start_index
return True
- def done(self):
- return (self.next_index-self.force_start_index >= len(self.objs))
+ def done(self, last_data_index):
+ return last_data_index >= self.end_index
def next(self):
- obj = self.objs[self.next_index-self.force_start_index]
-
- if self.outputs['image'].isConnected():
- data = {
- 'value': obj.load(directory=self.root_folder)
- }
- self.outputs['image'].write(data, self.next_index)
+ obj = self.objs[self.next_index - self.start_index]
+ # Output: vein_annotations (provide data at each iteration)
if self.outputs['vein_annotations'].isConnected():
- data = {
- 'value': obj.construct_vein_image(directory=self.root_folder)
- }
- self.outputs['vein_annotations'].write(data, self.next_index)
-
+ self.outputs['vein_annotations'].write(
+ {
+ 'value': obj.construct_vein_image(directory=self.root_folder)
+ },
+ self.next_index
+ )
+
+ # Output: ROI_annotations (provide data at each iteration)
if self.outputs['ROI_annotations'].isConnected():
- data = {
- 'value': obj.construct_ROI_image(directory=self.root_folder)
- }
- self.outputs['ROI_annotations'].write(data, self.next_index)
-
+ self.outputs['ROI_annotations'].write(
+ {
+ 'value': obj.construct_ROI_image(directory=self.root_folder)
+ },
+ self.next_index
+ )
+
+ # Output: alignment_annotations (provide data at each iteration)
if self.outputs['alignment_annotations'].isConnected():
- alignment_annotations = \
- obj.alignment_annotations(directory=self.root_folder)
+ alignment_annotations = obj.alignment_annotations(directory=self.root_folder)
+
coordinate_list = []
for annotation in alignment_annotations:
coordinate = {
- "y": np.int32(annotation[0]),
- "x": np.int32(annotation[1])
- }
+ "y": np.int32(annotation[0]),
+ "x": np.int32(annotation[1])
+ }
coordinate_list.append(coordinate)
- data = {'coordinate_list': coordinate_list}
- self.outputs['alignment_annotations'].write(data, self.next_index)
- self.next_index += 1
+ self.outputs['alignment_annotations'].write(
+ {
+ 'value': coordinate_list
+ },
+ self.next_index
+ )
+
+ # Output: image (provide data at each iteration)
+ if self.outputs['image'].isConnected():
+ self.outputs['image'].write(
+ {
+ 'value': obj.load(directory=self.root_folder)
+ },
+ self.next_index
+ )
+
+ # Determine the next data index that must be provided
+ self.next_index = 1 + min([ x.last_written_data_index for x in self.outputs
+ if x.isConnected() ]
+ )
+
return True
-"""
-# example for class AnnotationBenchmark to get only annotated, not mirrored
-# files (total count - 666):
+#----------------------------------------------------------
-import bob.db.biowave_v1
-db = bob.db.biowave_v1.Database()
-obj = db.objects(protocol="Idiap_1_1_R",
- annotated_images=True,
- imagedir="/idiap/project/biowave/biowave_v1/data/"
- )
-print(len(obj))
-"""
-
-"""
-protocol = "Idiap_1_5_R_BEAT_test"
-import bob.db.biowave_v1
-db = bob.db.biowave_v1.Database()
-files = db.objects(protocol=protocol,
- annotated_images=True,
- imagedir="/idiap/project/biowave/biowave_v1/data/",
- groups="dev",
- purposes="probe")
-
-"""
+
+def setup_tests():
+ # Install a mock methods
+ def mock_load(obj, directory=''):
+ return np.ndarray((10, 20), dtype=np.uint8)
+
+ def mock_construct_vein_image(obj, directory=''):
+ return np.ndarray((10, 20), dtype=np.uint8)
+
+ def mock_construct_ROI_image(obj, directory=''):
+ return np.ndarray((10, 20), dtype=np.uint8)
+
+ bob.db.biowave_v1.models.File.load = mock_load
+ bob.db.biowave_v1.models.File.construct_vein_image = mock_construct_vein_image
+ bob.db.biowave_v1.models.File.construct_ROI_image = mock_construct_ROI_image
+
+
+#----------------------------------------------------------
+
+
+# Test the behavior of the views (on fake data)
+if __name__ == '__main__':
+
+ setup_tests()
+
+ from beat.backend.python.database import DatabaseTester
+
+ DatabaseTester('View', View,
+ [
+ 'client_id',
+ 'image',
+ ],
+ parameters=dict(
+ protocol="Idiap_1_1_R_BEAT_test",
+ group="world",
+ ),
+ )
+
+ DatabaseTester('TemplateView', TemplateView,
+ [
+ 'client_id',
+ 'model_id',
+ 'image',
+ ],
+ parameters=dict(
+ protocol="Idiap_1_1_R_BEAT_test",
+ group="dev",
+ purpose="enroll",
+ ),
+ irregular_outputs=[
+ 'model_id',
+ ]
+ )
diff --git a/advanced/databases/biowave/1.rst b/advanced/databases/biowave/1.rst
index da3553a..1d6b587 100644
--- a/advanced/databases/biowave/1.rst
+++ b/advanced/databases/biowave/1.rst
@@ -1,4 +1,4 @@
-.. Copyright (c) 2016 Idiap Research Institute, http://www.idiap.ch/ ..
+.. Copyright (c) 2017 Idiap Research Institute, http://www.idiap.ch/ ..
.. Contact: beat.support@idiap.ch ..
.. ..
.. This file is part of the beat.examples module of the BEAT platform. ..
@@ -24,7 +24,7 @@ BIOWAVE Vein Database
Changelog
=========
-* **Version 1**, 10/Feb/2017:
+* **Version 1**, 30/Oct/2017:
- Initial release
diff --git a/advanced/databases/biowave/2.json b/advanced/databases/biowave/2.json
deleted file mode 100644
index 111a731..0000000
--- a/advanced/databases/biowave/2.json
+++ /dev/null
@@ -1,1502 +0,0 @@
-{
- "root_folder": "/idiap/project/biowave/biowave_v1/data",
- "description": "BIOWAVE Vein Database",
- "protocols": [
- {
- "name": "Idiap_1_1_R_BEAT_test",
- "template": "advanced_vein_recognition_2",
- "sets": [
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "template": "train",
- "parameters": {
- "protocol": "Idiap_1_1_R_BEAT_test",
- "group": "world"
- },
- "name": "train"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateView",
- "name": "dev_templates",
- "parameters": {
- "protocol": "Idiap_1_1_R_BEAT_test",
- "group": "dev",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "name": "dev_probes",
- "parameters": {
- "protocol": "Idiap_1_1_R_BEAT_test",
- "group": "dev",
- "purpose": "probe"
- },
- "template": "probe"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateView",
- "name": "eval_templates",
- "parameters": {
- "protocol": "Idiap_1_1_R_BEAT_test",
- "group": "eval",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "name": "eval_probes",
- "parameters": {
- "protocol": "Idiap_1_1_R_BEAT_test",
- "group": "eval",
- "purpose": "probe"
- },
- "template": "probe"
- }
- ]
- },
- {
- "name": "Idiap_5_5_R_BEAT_test",
- "template": "advanced_vein_recognition_2",
- "sets": [
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "template": "train",
- "parameters": {
- "protocol": "Idiap_5_5_R_BEAT_test",
- "group": "world"
- },
- "name": "train"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateView",
- "name": "dev_templates",
- "parameters": {
- "protocol": "Idiap_5_5_R_BEAT_test",
- "group": "dev",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "name": "dev_probes",
- "parameters": {
- "protocol": "Idiap_5_5_R_BEAT_test",
- "group": "dev",
- "purpose": "probe"
- },
- "template": "probe"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateView",
- "name": "eval_templates",
- "parameters": {
- "protocol": "Idiap_5_5_R_BEAT_test",
- "group": "eval",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "name": "eval_probes",
- "parameters": {
- "protocol": "Idiap_5_5_R_BEAT_test",
- "group": "eval",
- "purpose": "probe"
- },
- "template": "probe"
- }
- ]
- },
- {
- "name": "Idiap_1_5_R_BEAT_test",
- "template": "advanced_vein_recognition_2",
- "sets": [
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "template": "train",
- "parameters": {
- "protocol": "Idiap_1_5_R_BEAT_test",
- "group": "world"
- },
- "name": "train"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateView",
- "name": "dev_templates",
- "parameters": {
- "protocol": "Idiap_1_5_R_BEAT_test",
- "group": "dev",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "name": "dev_probes",
- "parameters": {
- "protocol": "Idiap_1_5_R_BEAT_test",
- "group": "dev",
- "purpose": "probe"
- },
- "template": "probe"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateView",
- "name": "eval_templates",
- "parameters": {
- "protocol": "Idiap_1_5_R_BEAT_test",
- "group": "eval",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "name": "eval_probes",
- "parameters": {
- "protocol": "Idiap_1_5_R_BEAT_test",
- "group": "eval",
- "purpose": "probe"
- },
- "template": "probe"
- }
- ]
- },
- {
- "name": "Idiap_1_1_R",
- "template": "advanced_vein_recognition_2",
- "sets": [
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "template": "train",
- "parameters": {
- "protocol": "Idiap_1_1_R",
- "group": "world"
- },
- "name": "train"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateView",
- "name": "dev_templates",
- "parameters": {
- "protocol": "Idiap_1_1_R",
- "group": "dev",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "name": "dev_probes",
- "parameters": {
- "protocol": "Idiap_1_1_R",
- "group": "dev",
- "purpose": "probe"
- },
- "template": "probe"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateView",
- "name": "eval_templates",
- "parameters": {
- "protocol": "Idiap_1_1_R",
- "group": "eval",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "name": "eval_probes",
- "parameters": {
- "protocol": "Idiap_1_1_R",
- "group": "eval",
- "purpose": "probe"
- },
- "template": "probe"
- }
- ]
- },
- {
- "name": "Idiap_1_5_R",
- "template": "advanced_vein_recognition_2",
- "sets": [
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "template": "train",
- "parameters": {
- "protocol": "Idiap_1_5_R",
- "group": "world"
- },
- "name": "train"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateView",
- "name": "dev_templates",
- "parameters": {
- "protocol": "Idiap_1_5_R",
- "group": "dev",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "name": "dev_probes",
- "parameters": {
- "protocol": "Idiap_1_5_R",
- "group": "dev",
- "purpose": "probe"
- },
- "template": "probe"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateView",
- "name": "eval_templates",
- "parameters": {
- "protocol": "Idiap_1_5_R",
- "group": "eval",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "name": "eval_probes",
- "parameters": {
- "protocol": "Idiap_1_5_R",
- "group": "eval",
- "purpose": "probe"
- },
- "template": "probe"
- }
- ]
- },
- {
- "name": "Idiap_5_5_R",
- "template": "advanced_vein_recognition_2",
- "sets": [
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "template": "train",
- "parameters": {
- "protocol": "Idiap_5_5_R",
- "group": "world"
- },
- "name": "train"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateView",
- "name": "dev_templates",
- "parameters": {
- "protocol": "Idiap_5_5_R",
- "group": "dev",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "name": "dev_probes",
- "parameters": {
- "protocol": "Idiap_5_5_R",
- "group": "dev",
- "purpose": "probe"
- },
- "template": "probe"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateView",
- "name": "eval_templates",
- "parameters": {
- "protocol": "Idiap_5_5_R",
- "group": "eval",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "name": "eval_probes",
- "parameters": {
- "protocol": "Idiap_5_5_R",
- "group": "eval",
- "purpose": "probe"
- },
- "template": "probe"
- }
- ]
- },
- {
- "name": "Idiap_1_1_L",
- "template": "advanced_vein_recognition_2",
- "sets": [
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "template": "train",
- "parameters": {
- "protocol": "Idiap_1_1_L",
- "group": "world"
- },
- "name": "train"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateView",
- "name": "dev_templates",
- "parameters": {
- "protocol": "Idiap_1_1_L",
- "group": "dev",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "name": "dev_probes",
- "parameters": {
- "protocol": "Idiap_1_1_L",
- "group": "dev",
- "purpose": "probe"
- },
- "template": "probe"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateView",
- "name": "eval_templates",
- "parameters": {
- "protocol": "Idiap_1_1_L",
- "group": "eval",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "name": "eval_probes",
- "parameters": {
- "protocol": "Idiap_1_1_L",
- "group": "eval",
- "purpose": "probe"
- },
- "template": "probe"
- }
- ]
- },
- {
- "name": "Idiap_1_5_L",
- "template": "advanced_vein_recognition_2",
- "sets": [
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "template": "train",
- "parameters": {
- "protocol": "Idiap_1_5_L",
- "group": "world"
- },
- "name": "train"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateView",
- "name": "dev_templates",
- "parameters": {
- "protocol": "Idiap_1_5_L",
- "group": "dev",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "name": "dev_probes",
- "parameters": {
- "protocol": "Idiap_1_5_L",
- "group": "dev",
- "purpose": "probe"
- },
- "template": "probe"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateView",
- "name": "eval_templates",
- "parameters": {
- "protocol": "Idiap_1_5_L",
- "group": "eval",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "name": "eval_probes",
- "parameters": {
- "protocol": "Idiap_1_5_L",
- "group": "eval",
- "purpose": "probe"
- },
- "template": "probe"
- }
- ]
- },
- {
- "name": "Idiap_5_5_L",
- "template": "advanced_vein_recognition_2",
- "sets": [
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "template": "train",
- "parameters": {
- "protocol": "Idiap_5_5_L",
- "group": "world"
- },
- "name": "train"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateView",
- "name": "dev_templates",
- "parameters": {
- "protocol": "Idiap_5_5_L",
- "group": "dev",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "name": "dev_probes",
- "parameters": {
- "protocol": "Idiap_5_5_L",
- "group": "dev",
- "purpose": "probe"
- },
- "template": "probe"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateView",
- "name": "eval_templates",
- "parameters": {
- "protocol": "Idiap_5_5_L",
- "group": "eval",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "name": "eval_probes",
- "parameters": {
- "protocol": "Idiap_5_5_L",
- "group": "eval",
- "purpose": "probe"
- },
- "template": "probe"
- }
- ]
- },
- {
- "name": "Idiap_1_1_R_less",
- "template": "advanced_vein_recognition_2",
- "sets": [
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "template": "train",
- "parameters": {
- "protocol": "Idiap_1_1_R_less",
- "group": "world"
- },
- "name": "train"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateView",
- "name": "dev_templates",
- "parameters": {
- "protocol": "Idiap_1_1_R_less",
- "group": "dev",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "name": "dev_probes",
- "parameters": {
- "protocol": "Idiap_1_1_R_less",
- "group": "dev",
- "purpose": "probe"
- },
- "template": "probe"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateView",
- "name": "eval_templates",
- "parameters": {
- "protocol": "Idiap_1_1_R_less",
- "group": "eval",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "name": "eval_probes",
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- "protocol": "Idiap_1_1_R_less",
- "group": "eval",
- "purpose": "probe"
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- "template": "probe"
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- ]
- },
- {
- "name": "Idiap_1_5_R_less",
- "template": "advanced_vein_recognition_2",
- "sets": [
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "template": "train",
- "parameters": {
- "protocol": "Idiap_1_5_R_less",
- "group": "world"
- },
- "name": "train"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateView",
- "name": "dev_templates",
- "parameters": {
- "protocol": "Idiap_1_5_R_less",
- "group": "dev",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "name": "dev_probes",
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- "protocol": "Idiap_1_5_R_less",
- "group": "dev",
- "purpose": "probe"
- },
- "template": "probe"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateView",
- "name": "eval_templates",
- "parameters": {
- "protocol": "Idiap_1_5_R_less",
- "group": "eval",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "name": "eval_probes",
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- "protocol": "Idiap_1_5_R_less",
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- "purpose": "probe"
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- ]
- },
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- "name": "Idiap_5_5_R_less",
- "template": "advanced_vein_recognition_2",
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- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "template": "train",
- "parameters": {
- "protocol": "Idiap_5_5_R_less",
- "group": "world"
- },
- "name": "train"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateView",
- "name": "dev_templates",
- "parameters": {
- "protocol": "Idiap_5_5_R_less",
- "group": "dev",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "name": "dev_probes",
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- "protocol": "Idiap_5_5_R_less",
- "group": "dev",
- "purpose": "probe"
- },
- "template": "probe"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateView",
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- "protocol": "Idiap_5_5_R_less",
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- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "View",
- "name": "eval_probes",
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- },
- "template": "probe"
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- {
- "name": "Idiap_1_1_R_annotations_BEAT_test",
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- "sets": [
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "ViewAnnotations",
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- "parameters": {
- "protocol": "Idiap_1_1_R_BEAT_test",
- "group": "world"
- },
- "name": "train"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateViewAnnotations",
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- "parameters": {
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- "group": "dev",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "ViewAnnotations",
- "name": "dev_probes",
- "parameters": {
- "protocol": "Idiap_1_1_R_BEAT_test",
- "group": "dev",
- "purpose": "probe"
- },
- "template": "probe"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
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- "view": "TemplateViewAnnotations",
- "name": "eval_templates",
- "parameters": {
- "protocol": "Idiap_1_1_R_BEAT_test",
- "group": "eval",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateViewAnnotations",
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- "parameters": {
- "protocol": "Idiap_1_1_R_BEAT_test",
- "group": "eval",
- "purpose": "probe"
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- "template": "probe"
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- ]
- },
- {
- "name": "Idiap_2_1_R_annotations_BEAT_test",
- "template": "advanced_vein_annotations",
- "sets": [
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "ViewAnnotations",
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- "parameters": {
- "protocol": "Idiap_5_5_R_BEAT_test",
- "group": "world"
- },
- "name": "train"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
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- "view": "TemplateViewAnnotations",
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- "parameters": {
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- "group": "dev",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "ViewAnnotations",
- "name": "dev_probes",
- "parameters": {
- "protocol": "Idiap_5_5_R_BEAT_test",
- "group": "dev",
- "purpose": "probe"
- },
- "template": "probe"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
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- "view": "TemplateViewAnnotations",
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- "parameters": {
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- "group": "eval",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
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- "view": "TemplateViewAnnotations",
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- "parameters": {
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- },
- {
- "name": "Idiap_1_1_R_annotations",
- "template": "advanced_vein_annotations",
- "sets": [
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
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- "parameters": {
- "protocol": "Idiap_1_1_R",
- "group": "world"
- },
- "name": "train"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
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- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
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- "view": "ViewAnnotations",
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- },
- "template": "probe"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
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- "view": "TemplateViewAnnotations",
- "name": "eval_templates",
- "parameters": {
- "protocol": "Idiap_1_1_R",
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- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
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- "view": "TemplateViewAnnotations",
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- "parameters": {
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- },
- {
- "name": "Idiap_2_1_R_annotations",
- "template": "advanced_vein_annotations",
- "sets": [
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "ViewAnnotations",
- "template": "train",
- "parameters": {
- "protocol": "Idiap_5_5_R",
- "group": "world"
- },
- "name": "train"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateViewAnnotations",
- "name": "dev_templates",
- "parameters": {
- "protocol": "Idiap_5_5_R",
- "group": "dev",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "ViewAnnotations",
- "name": "dev_probes",
- "parameters": {
- "protocol": "Idiap_5_5_R",
- "group": "dev",
- "purpose": "probe"
- },
- "template": "probe"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateViewAnnotations",
- "name": "eval_templates",
- "parameters": {
- "protocol": "Idiap_5_5_R",
- "group": "eval",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateViewAnnotations",
- "name": "eval_probes",
- "parameters": {
- "protocol": "Idiap_5_5_R",
- "group": "eval",
- "purpose": "probe"
- },
- "template": "probe"
- }
- ]
- },
- {
- "name": "Idiap_1_1_L_annotations",
- "template": "advanced_vein_annotations",
- "sets": [
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "ViewAnnotations",
- "template": "train",
- "parameters": {
- "protocol": "Idiap_1_1_L",
- "group": "world"
- },
- "name": "train"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateViewAnnotations",
- "name": "dev_templates",
- "parameters": {
- "protocol": "Idiap_1_1_L",
- "group": "dev",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "ViewAnnotations",
- "name": "dev_probes",
- "parameters": {
- "protocol": "Idiap_1_1_L",
- "group": "dev",
- "purpose": "probe"
- },
- "template": "probe"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateViewAnnotations",
- "name": "eval_templates",
- "parameters": {
- "protocol": "Idiap_1_1_L",
- "group": "eval",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateViewAnnotations",
- "name": "eval_probes",
- "parameters": {
- "protocol": "Idiap_1_1_L",
- "group": "eval",
- "purpose": "probe"
- },
- "template": "probe"
- }
- ]
- },
- {
- "name": "Idiap_2_1_L_annotations",
- "template": "advanced_vein_annotations",
- "sets": [
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "ViewAnnotations",
- "template": "train",
- "parameters": {
- "protocol": "Idiap_5_5_L",
- "group": "world"
- },
- "name": "train"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateViewAnnotations",
- "name": "dev_templates",
- "parameters": {
- "protocol": "Idiap_5_5_L",
- "group": "dev",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "ViewAnnotations",
- "name": "dev_probes",
- "parameters": {
- "protocol": "Idiap_5_5_L",
- "group": "dev",
- "purpose": "probe"
- },
- "template": "probe"
- },
- {
- "outputs": {
- "model_id": "{{ system_user.username }}/text/1",
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateViewAnnotations",
- "name": "eval_templates",
- "parameters": {
- "protocol": "Idiap_5_5_L",
- "group": "eval",
- "purpose": "enroll"
- },
- "template": "enroll"
- },
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1",
- "client_id": "{{ system_user.username }}/uint64/1"
- },
- "view": "TemplateViewAnnotations",
- "name": "eval_probes",
- "parameters": {
- "protocol": "Idiap_5_5_L",
- "group": "eval",
- "purpose": "probe"
- },
- "template": "probe"
- }
- ]
- },
- {
- "name": "annotation_benchmark",
- "template": "advanced_annotation_benchmark",
- "sets": [
- {
- "outputs": {
- "image": "{{ system_user.username }}/array_2d_uint8/1",
- "vein_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "ROI_annotations": "{{ system_user.username }}/array_2d_uint8/1",
- "alignment_annotations": "{{ user.username }}/coordinate_list/1"
- },
- "view": "AnnotationBenchmark",
- "template": "annotation_benchmark",
- "parameters": {
- "protocol": "Idiap_1_1_R"
- },
- "name": "annotations"
- }
- ]
- }
- ]
-}
diff --git a/advanced/databases/biowave/2.py b/advanced/databases/biowave/2.py
deleted file mode 100644
index 05f6cbe..0000000
--- a/advanced/databases/biowave/2.py
+++ /dev/null
@@ -1,745 +0,0 @@
-###############################################################################
-# #
-# Copyright (c) 2017 Idiap Research Institute, http://www.idiap.ch/ #
-# Contact: beat.support@idiap.ch #
-# #
-# This file is part of the beat.examples module of the BEAT platform. #
-# #
-# Commercial License Usage #
-# Licensees holding valid commercial BEAT licenses may use this file in #
-# accordance with the terms contained in a written agreement between you #
-# and Idiap. For further information contact tto@idiap.ch #
-# #
-# Alternatively, this file may be used under the terms of the GNU Affero #
-# Public License version 3 as published by the Free Software and appearing #
-# in the file LICENSE.AGPL included in the packaging of this file. #
-# The BEAT platform is distributed in the hope that it will be useful, but #
-# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY #
-# or FITNESS FOR A PARTICULAR PURPOSE. #
-# #
-# You should have received a copy of the GNU Affero Public License along #
-# with the BEAT platform. If not, see http://www.gnu.org/licenses/. #
-# #
-###############################################################################
-
-import os
-import numpy as np
-import bob.io.base
-import bob.io.image
-import bob.db.biowave_v1
-
-
-#----------------------------------------------------------
-
-
-def get_client_end_index(objs, client_id, client_start_index,
- start_index, end_index):
- client_end_index = client_start_index
-
- while client_end_index + 1 <= end_index:
- obj = objs[client_end_index + 1 - start_index]
-
- if isinstance(obj, tuple):
- obj = obj[1]
-
- if obj.client_id != client_id:
- return client_end_index
-
- client_end_index += 1
-
- return end_index
-
-
-#----------------------------------------------------------
-
-
-def get_model_end_index(objs, model_id, model_start_index,
- start_index, end_index):
- model_end_index = model_start_index
-
- while model_end_index + 1 <= end_index:
- obj = objs[model_end_index + 1 - start_index]
-
- if obj.model_id != model_id:
- return model_end_index
-
- model_end_index += 1
-
- return end_index
-
-
-#----------------------------------------------------------
-
-
-class View:
- """Outputs:
- - image: "{{ system_user.username }}/array_2d_uint8/1"
- - client_id: "{{ system_user.username }}/uint64/1"
-
- Several "image" are associated with a given "client_id".
-
- --------------- --------------- --------------- --------------- --------------- ---------------
- | image | | image | | image | | image | | image | | image |
- --------------- --------------- --------------- --------------- --------------- ---------------
- ----------------------------------------------- -----------------------------------------------
- | client_id | | client_id |
- ----------------------------------------------- -----------------------------------------------
- """
-
- def setup(self, root_folder, outputs, parameters, force_start_index=None,
- force_end_index=None):
-
- # Initialisations
- self.root_folder = root_folder
- self.outputs = outputs
- self.parameters = parameters
-
- # Open the database and load the objects to provide via the outputs
- self.db = bob.db.biowave_v1.Database()
-
- self.objs = sorted(self.db.objects(protocol=self.parameters['protocol'],
- groups=[self.parameters['group']],
- purposes=self.parameters.get('purpose', None),
- annotated_images=False,
- imagedir=self.root_folder),
- key=lambda x: (x.client_id, x.id))
-
- # Determine the range of indices that must be provided
- self.start_index = force_start_index if force_start_index is not None else 0
- self.end_index = force_end_index if force_end_index is not None else len(self.objs) - 1
-
- self.objs = self.objs[self.start_index : self.end_index + 1]
-
- self.next_index = self.start_index
-
- return True
-
-
- def done(self, last_data_index):
- return last_data_index >= self.end_index
-
-
- def next(self):
- obj = self.objs[self.next_index - self.start_index]
-
- # Output: client_id (only provide data when the client_id change)
- if self.outputs['client_id'].isConnected() and \
- self.outputs['client_id'].last_written_data_index < self.next_index:
-
- client_end_index = get_client_end_index(self.objs, obj.client_id,
- self.next_index,
- self.start_index,
- self.end_index)
-
- self.outputs['client_id'].write(
- {
- 'value': np.uint64(obj.client_id)
- },
- client_end_index
- )
-
- # Output: image (provide data at each iteration)
- if self.outputs['image'].isConnected():
- self.outputs['image'].write(
- {
- 'value': obj.load(directory=self.root_folder)
- },
- self.next_index
- )
-
- # Determine the next data index that must be provided
- self.next_index = 1 + min([ x.last_written_data_index for x in self.outputs
- if x.isConnected() ]
- )
-
- return True
-
-
-#----------------------------------------------------------
-
-
-class TemplateView:
- """Outputs:
- - image: "{{ system_user.username }}/array_2d_uint8/1"
- - client_id: "{{ system_user.username }}/uint64/1"
- - model_id: "{{ system_user.username }}/text/1"
-
- Several "image" are associated with a given "model_id".
- Several "model_id" are associated with a given "client_id".
-
- --------------- --------------- --------------- --------------- --------------- ---------------
- | image | | image | | image | | image | | image | | image |
- --------------- --------------- --------------- --------------- --------------- ---------------
- ----------------------------------------------- -----------------------------------------------
- | model_id | | model_id |
- ----------------------------------------------- -----------------------------------------------
- -----------------------------------------------------------------------------------------------
- | client_id |
- -----------------------------------------------------------------------------------------------
-
- Note: for this particular database, there is only one "image"
- per "model_id".
- """
-
- def setup(self, root_folder, outputs, parameters, force_start_index=None,
- force_end_index=None):
-
- # Initialisations
- self.root_folder = root_folder
- self.outputs = outputs
- self.parameters = parameters
-
- # Open the database and load the objects to provide via the outputs
- self.db = bob.db.biowave_v1.Database()
-
- self.objs = sorted(self.db.objects(protocol=self.parameters['protocol'],
- purposes=self.parameters['purpose'],
- groups=[self.parameters['group']],
- annotated_images=False,
- imagedir=self.root_folder),
- key=lambda x: (x.client_id, x.model_id, x.id))
-
- # Determine the range of indices that must be provided
- self.start_index = force_start_index if force_start_index is not None else 0
- self.end_index = force_end_index if force_end_index is not None else len(self.objs) - 1
-
- self.objs = self.objs[self.start_index : self.end_index + 1]
-
- self.next_index = self.start_index
-
- return True
-
-
- def done(self, last_data_index):
- return last_data_index >= self.end_index
-
-
- def next(self):
- obj = self.objs[self.next_index - self.start_index]
-
- # Output: model_id (only provide data when the model_id change)
- if self.outputs['model_id'].isConnected() and \
- self.outputs['model_id'].last_written_data_index < self.next_index:
-
- model_end_index = get_model_end_index(self.objs, obj.model_id,
- self.next_index,
- self.start_index,
- self.end_index)
-
- self.outputs['model_id'].write(
- {
- 'text': obj.model_id.encode('utf-8')
- },
- model_end_index
- )
-
- # Output: client_id (only provide data when the client_id change)
- if self.outputs['client_id'].isConnected() and \
- self.outputs['client_id'].last_written_data_index < self.next_index:
-
- # Please pay attention - we can use the object CLIENT ID as long as we
- # don't use both hands data of the same client in the same protocol.
- client_end_index = get_client_end_index(self.objs, obj.client_id,
- self.next_index,
- self.start_index,
- self.end_index)
-
- self.outputs['client_id'].write(
- {
- 'value': np.uint64(obj.client_id)
- },
- client_end_index
- )
-
- # Output: image (provide data at each iteration)
- if self.outputs['image'].isConnected():
- self.outputs['image'].write(
- {
- 'value': obj.load(directory=self.root_folder)
- },
- self.next_index
- )
-
- # Determine the next data index that must be provided
- self.next_index = 1 + min([ x.last_written_data_index for x in self.outputs
- if x.isConnected() ]
- )
-
- return True
-
-
-#----------------------------------------------------------
-
-
-class ViewAnnotations:
- """Outputs:
- - image: "{{ system_user.username }}/array_2d_uint8/1"
- - vein_annotations: "{{ system_user.username }}/array_2d_uint8/1"
- - ROI_annotations: "{{ system_user.username }}/array_2d_uint8/1"
- - alignment_annotations: "{{ user.username }}/coordinate_list/1"
- - client_id: "{{ system_user.username }}/uint64/1"
-
- One "vein_annotations" are associated with a given "image".
- One "ROI_annotations" are associated with a given "image".
- One "alignment_annotations" are associated with a given "image".
- Several "image" are associated with a given "client_id".
-
- ------------------------- ------------------------- ------------------------- -------------------------
- | image | | image | | image | | image |
- ------------------------- ------------------------- ------------------------- -------------------------
- ------------------------- ------------------------- ------------------------- -------------------------
- | vein_annotations | | vein_annotations | | vein_annotations | | vein_annotations |
- ------------------------- ------------------------- ------------------------- -------------------------
- ------------------------- ------------------------- ------------------------- -------------------------
- | ROI_annotations | | ROI_annotations | | ROI_annotations | | ROI_annotations |
- ------------------------- ------------------------- ------------------------- -------------------------
- ------------------------- ------------------------- ------------------------- -------------------------
- | alignment_annotations | | alignment_annotations | | alignment_annotations | | alignment_annotations |
- ------------------------- ------------------------- ------------------------- -------------------------
- --------------------------------------------------- ---------------------------------------------------
- | client_id | | client_id |
- --------------------------------------------------- ---------------------------------------------------
- """
-
- def setup(self, root_folder, outputs, parameters, force_start_index=None,
- force_end_index=None):
-
- # Initialisations
- self.root_folder = root_folder
- self.outputs = outputs
- self.parameters = parameters
-
- # Open the database and load the objects to provide via the outputs
- self.db = bob.db.biowave_v1.Database()
-
- self.objs = sorted(self.db.objects(protocol=self.parameters['protocol'],
- groups=[self.parameters['group']],
- purposes=self.parameters.get('purpose', None),
- annotated_images=True,
- imagedir=self.root_folder),
- key=lambda x: (x.client_id, x.id))
-
- # Determine the range of indices that must be provided
- self.start_index = force_start_index if force_start_index is not None else 0
- self.end_index = force_end_index if force_end_index is not None else len(self.objs) - 1
-
- self.objs = self.objs[self.start_index : self.end_index + 1]
-
- self.next_index = self.start_index
-
- return True
-
-
- def done(self, last_data_index):
- return last_data_index >= self.end_index
-
-
- def next(self):
- obj = self.objs[self.next_index - self.start_index]
-
- # Output: client_id (only provide data when the client_id change)
- if self.outputs['client_id'].isConnected() and \
- self.outputs['client_id'].last_written_data_index < self.next_index:
-
- client_end_index = get_client_end_index(self.objs, obj.client_id,
- self.next_index,
- self.start_index,
- self.end_index)
-
- self.outputs['client_id'].write(
- {
- 'value': np.uint64(obj.client_id)
- },
- client_end_index
- )
-
- # Output: vein_annotations (provide data at each iteration)
- if self.outputs['vein_annotations'].isConnected():
- self.outputs['vein_annotations'].write(
- {
- 'value': obj.construct_vein_image(directory=self.root_folder)
- },
- self.next_index
- )
-
- # Output: ROI_annotations (provide data at each iteration)
- if self.outputs['ROI_annotations'].isConnected():
- self.outputs['ROI_annotations'].write(
- {
- 'value': obj.construct_ROI_image(directory=self.root_folder)
- },
- self.next_index
- )
-
- # Output: alignment_annotations (provide data at each iteration)
- if self.outputs['alignment_annotations'].isConnected():
- alignment_annotations = obj.alignment_annotations(directory=self.root_folder)
-
- coordinate_list = []
- for annotation in alignment_annotations:
- coordinate = {
- "y": np.int32(annotation[0]),
- "x": np.int32(annotation[1])
- }
- coordinate_list.append(coordinate)
-
- self.outputs['alignment_annotations'].write(
- {
- 'coordinate_list': coordinate_list
- },
- self.next_index
- )
-
- # Output: image (provide data at each iteration)
- if self.outputs['image'].isConnected():
- self.outputs['image'].write(
- {
- 'value': obj.load(directory=self.root_folder)
- },
- self.next_index
- )
-
- # Determine the next data index that must be provided
- self.next_index = 1 + min([ x.last_written_data_index for x in self.outputs
- if x.isConnected() ]
- )
-
- return True
-
-
-#----------------------------------------------------------
-
-
-class TemplateViewAnnotations:
- """Outputs:
- - image: "{{ system_user.username }}/array_2d_uint8/1"
- - vein_annotations: "{{ system_user.username }}/array_2d_uint8/1"
- - ROI_annotations: "{{ system_user.username }}/array_2d_uint8/1"
- - alignment_annotations: "{{ user.username }}/coordinate_list/1"
- - model_id: "{{ system_user.username }}/model_id/1"
- - client_id: "{{ system_user.username }}/uint64/1"
-
- One "vein_annotations" are associated with a given "image".
- One "ROI_annotations" are associated with a given "image".
- One "alignment_annotations" are associated with a given "image".
- Several "image" are associated with a given "model_id".
- Several "model_id" are associated with a given "client_id".
-
- ------------------------- ------------------------- ------------------------- -------------------------
- | image | | image | | image | | image |
- ------------------------- ------------------------- ------------------------- -------------------------
- ------------------------- ------------------------- ------------------------- -------------------------
- | vein_annotations | | vein_annotations | | vein_annotations | | vein_annotations |
- ------------------------- ------------------------- ------------------------- -------------------------
- ------------------------- ------------------------- ------------------------- -------------------------
- | ROI_annotations | | ROI_annotations | | ROI_annotations | | ROI_annotations |
- ------------------------- ------------------------- ------------------------- -------------------------
- ------------------------- ------------------------- ------------------------- -------------------------
- | alignment_annotations | | alignment_annotations | | alignment_annotations | | alignment_annotations |
- ------------------------- ------------------------- ------------------------- -------------------------
- --------------------------------------------------- ---------------------------------------------------
- | model_id | | model_id |
- --------------------------------------------------- ---------------------------------------------------
- -------------------------------------------------------------------------------------------------------
- | client_id |
- -------------------------------------------------------------------------------------------------------
-
- Note: for this particular database, there is only one "image"
- per "model_id".
- """
-
- def setup(self, root_folder, outputs, parameters, force_start_index=None,
- force_end_index=None):
-
- # Initialisations
- self.root_folder = root_folder
- self.outputs = outputs
- self.parameters = parameters
-
- # Open the database and load the objects to provide via the outputs
- self.db = bob.db.biowave_v1.Database()
-
- self.objs = sorted(self.db.objects(protocol=self.parameters['protocol'],
- purposes=self.parameters['purpose'],
- groups=[self.parameters['group']],
- annotated_images=True,
- imagedir=self.root_folder),
- key=lambda x: (x.client_id, x.model_id, x.id))
-
- # Determine the range of indices that must be provided
- self.start_index = force_start_index if force_start_index is not None else 0
- self.end_index = force_end_index if force_end_index is not None else len(self.objs) - 1
-
- self.objs = self.objs[self.start_index : self.end_index + 1]
-
- self.next_index = self.start_index
-
- return True
-
-
- def done(self, last_data_index):
- return last_data_index >= self.end_index
-
-
- def next(self):
- obj = self.objs[self.next_index - self.start_index]
-
- # Output: model_id (only provide data when the model_id change)
- if self.outputs['model_id'].isConnected() and \
- self.outputs['model_id'].last_written_data_index < self.next_index:
-
- model_end_index = get_model_end_index(self.objs, obj.model_id,
- self.next_index,
- self.start_index,
- self.end_index)
-
- self.outputs['model_id'].write(
- {
- 'text': obj.model_id.encode('utf-8')
- },
- model_end_index
- )
-
- # Output: client_id (only provide data when the client_id change)
- if self.outputs['client_id'].isConnected() and \
- self.outputs['client_id'].last_written_data_index < self.next_index:
-
- # Please pay attention - we can use the object CLIENT ID as long as we
- # don't use both hands data of the same client in the same protocol.
- client_end_index = get_client_end_index(self.objs, obj.client_id,
- self.next_index,
- self.start_index,
- self.end_index)
-
- self.outputs['client_id'].write(
- {
- 'value': np.uint64(obj.client_id)
- },
- client_end_index
- )
-
- # Output: vein_annotations (provide data at each iteration)
- if self.outputs['vein_annotations'].isConnected():
- self.outputs['vein_annotations'].write(
- {
- 'value': obj.construct_vein_image(directory=self.root_folder)
- },
- self.next_index
- )
-
- # Output: ROI_annotations (provide data at each iteration)
- if self.outputs['ROI_annotations'].isConnected():
- self.outputs['ROI_annotations'].write(
- {
- 'value': obj.construct_ROI_image(directory=self.root_folder)
- },
- self.next_index
- )
-
- # Output: alignment_annotations (provide data at each iteration)
- if self.outputs['alignment_annotations'].isConnected():
- alignment_annotations = obj.alignment_annotations(directory=self.root_folder)
-
- coordinate_list = []
- for annotation in alignment_annotations:
- coordinate = {
- "y": np.int32(annotation[0]),
- "x": np.int32(annotation[1])
- }
- coordinate_list.append(coordinate)
-
- self.outputs['alignment_annotations'].write(
- {
- 'coordinate_list': coordinate_list
- },
- self.next_index
- )
-
- # Output: image (provide data at each iteration)
- if self.outputs['image'].isConnected():
- self.outputs['image'].write(
- {
- 'value': obj.load(directory=self.root_folder)
- },
- self.next_index
- )
-
- # Determine the next data index that must be provided
- self.next_index = 1 + min([ x.last_written_data_index for x in self.outputs
- if x.isConnected() ]
- )
-
- return True
-
-
-#----------------------------------------------------------
-
-
-class AnnotationBenchmark:
- """Outputs:
- - image: "{{ system_user.username }}/array_2d_uint8/1"
- - vein_annotations: "{{ system_user.username }}/array_2d_uint8/1"
- - ROI_annotations: "{{ system_user.username }}/array_2d_uint8/1"
- - alignment_annotations: "{{ user.username }}/coordinate_list/1"
-
- One "vein_annotations" are associated with a given "image".
- One "ROI_annotations" are associated with a given "image".
- One "alignment_annotations" are associated with a given "image".
-
- ------------------------- ------------------------- ------------------------- -------------------------
- | image | | image | | image | | image |
- ------------------------- ------------------------- ------------------------- -------------------------
- ------------------------- ------------------------- ------------------------- -------------------------
- | vein_annotations | | vein_annotations | | vein_annotations | | vein_annotations |
- ------------------------- ------------------------- ------------------------- -------------------------
- ------------------------- ------------------------- ------------------------- -------------------------
- | ROI_annotations | | ROI_annotations | | ROI_annotations | | ROI_annotations |
- ------------------------- ------------------------- ------------------------- -------------------------
- ------------------------- ------------------------- ------------------------- -------------------------
- | alignment_annotations | | alignment_annotations | | alignment_annotations | | alignment_annotations |
- ------------------------- ------------------------- ------------------------- -------------------------
- """
-
- def setup(self, root_folder, outputs, parameters, force_start_index=None,
- force_end_index=None):
-
- # Initialisations
- self.root_folder = root_folder
- self.outputs = outputs
- self.parameters = parameters
-
- # Open the database and load the objects to provide via the outputs
- self.db = bob.db.biowave_v1.Database()
-
- self.objs = sorted(self.db.objects(protocol=self.parameters['protocol'],
- annotated_images=True,
- imagedir=self.root_folder),
- key=lambda x: x.id)
-
- # Determine the range of indices that must be provided
- self.start_index = force_start_index if force_start_index is not None else 0
- self.end_index = force_end_index if force_end_index is not None else len(self.objs) - 1
-
- self.objs = self.objs[self.start_index : self.end_index + 1]
-
- self.next_index = self.start_index
-
- return True
-
-
- def done(self, last_data_index):
- return last_data_index >= self.end_index
-
-
- def next(self):
- obj = self.objs[self.next_index - self.start_index]
-
- # Output: vein_annotations (provide data at each iteration)
- if self.outputs['vein_annotations'].isConnected():
- self.outputs['vein_annotations'].write(
- {
- 'value': obj.construct_vein_image(directory=self.root_folder)
- },
- self.next_index
- )
-
- # Output: ROI_annotations (provide data at each iteration)
- if self.outputs['ROI_annotations'].isConnected():
- self.outputs['ROI_annotations'].write(
- {
- 'value': obj.construct_ROI_image(directory=self.root_folder)
- },
- self.next_index
- )
-
- # Output: alignment_annotations (provide data at each iteration)
- if self.outputs['alignment_annotations'].isConnected():
- alignment_annotations = obj.alignment_annotations(directory=self.root_folder)
-
- coordinate_list = []
- for annotation in alignment_annotations:
- coordinate = {
- "y": np.int32(annotation[0]),
- "x": np.int32(annotation[1])
- }
- coordinate_list.append(coordinate)
-
- self.outputs['alignment_annotations'].write(
- {
- 'coordinate_list': coordinate_list
- },
- self.next_index
- )
-
- # Output: image (provide data at each iteration)
- if self.outputs['image'].isConnected():
- self.outputs['image'].write(
- {
- 'value': obj.load(directory=self.root_folder)
- },
- self.next_index
- )
-
- # Determine the next data index that must be provided
- self.next_index = 1 + min([ x.last_written_data_index for x in self.outputs
- if x.isConnected() ]
- )
-
- return True
-
-
-#----------------------------------------------------------
-
-
-def setup_tests():
- # Install a mock methods
- def mock_load(obj, directory=''):
- return np.ndarray((10, 20), dtype=np.uint8)
-
- def mock_construct_vein_image(obj, directory=''):
- return np.ndarray((10, 20), dtype=np.uint8)
-
- def mock_construct_ROI_image(obj, directory=''):
- return np.ndarray((10, 20), dtype=np.uint8)
-
- bob.db.biowave_v1.models.File.load = mock_load
- bob.db.biowave_v1.models.File.construct_vein_image = mock_construct_vein_image
- bob.db.biowave_v1.models.File.construct_ROI_image = mock_construct_ROI_image
-
-
-#----------------------------------------------------------
-
-
-# Test the behavior of the views (on fake data)
-if __name__ == '__main__':
-
- setup_tests()
-
- from beat.backend.python.database import DatabaseTester
-
- DatabaseTester('View', View,
- [
- 'client_id',
- 'image',
- ],
- parameters=dict(
- protocol="Idiap_1_1_R_BEAT_test",
- group="world",
- ),
- )
-
- DatabaseTester('TemplateView', TemplateView,
- [
- 'client_id',
- 'model_id',
- 'image',
- ],
- parameters=dict(
- protocol="Idiap_1_1_R_BEAT_test",
- group="dev",
- purpose="enroll",
- ),
- irregular_outputs=[
- 'model_id',
- ]
- )
diff --git a/advanced/databases/biowave/2.rst b/advanced/databases/biowave/2.rst
deleted file mode 100644
index 83b1b8e..0000000
--- a/advanced/databases/biowave/2.rst
+++ /dev/null
@@ -1,208 +0,0 @@
-.. Copyright (c) 2016 Idiap Research Institute, http://www.idiap.ch/ ..
-.. Contact: beat.support@idiap.ch ..
-.. ..
-.. This file is part of the beat.examples module of the BEAT platform. ..
-.. ..
-.. Commercial License Usage ..
-.. Licensees holding valid commercial BEAT licenses may use this file in ..
-.. accordance with the terms contained in a written agreement between you ..
-.. and Idiap. For further information contact tto@idiap.ch ..
-.. ..
-.. Alternatively, this file may be used under the terms of the GNU Affero ..
-.. Public License version 3 as published by the Free Software and appearing ..
-.. in the file LICENSE.AGPL included in the packaging of this file. ..
-.. The BEAT platform is distributed in the hope that it will be useful, but ..
-.. WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY ..
-.. or FITNESS FOR A PARTICULAR PURPOSE. ..
-.. ..
-.. You should have received a copy of the GNU Affero Public License along ..
-.. with the BEAT platform. If not, see http://www.gnu.org/licenses/. ..
-
-BIOWAVE Vein Database
----------------------
-
-Changelog
-=========
-
-* **Version 2**, 30/Oct/2017:
-
- - Port to beat.backend.python v1.4.2
-
-* **Version 1**, 10/Feb/2017:
-
- - Initial release
-
-
-Description
-===========
-
-
-The ``BIOWAVE`` database contains wrist vein images that are acquired using
-BIOWATCH biometric sensor. For each subject of the database there are 3 session
-images (sessions were held at least 24 hours apart). Each session consists of 5
-attempts, in each attempt 5 images were acquired, meaning, that there are
-``3 sessions x 5 attempts x 5 images = 75`` images per each person's hand,
-``75 x 2 images`` per person.
-
-Images were previously manually evaluated, and if any of the 75 one hand's
-images were unusable (too blurred, veins couldn't be seen, etc), than all hand
-data were discarded. That is way some persons has only 1 hand's images in the
-database.
-
-Statistics of the data - in total 111 hands:
-
-1) Users with both hands images - 53
-2) Users with only R hand images - 4
-3) Users with only L hand images - 1
-
-
-
-Data division in ``groups`` and ``purposes``
-############################################
-
-
-In the BIOWAVE database there are following groups and purposes:
-
-
-+-------------+-----------+-----------------------+------------------------+
-| **groups** | ``world`` | ``dev`` | ``eval`` |
-+-------------+-----------+-----------------------+------------------------+
-|**purposes** | ``train`` |``enroll`` / ``probe`` | ``enroll`` / ``probe`` |
-+-------------+-----------+-----------------------+------------------------+
-
-
-Data are divided into training, development and evolution data sets:
-
-1) ``dev`` data set -- ``20`` persons with both hand images;
-2) ``eval`` data set -- ``20`` persons with both hand images;
-3) ``world`` data set -- the rest of ``13`` persons with both hand images + ``4`` persons with only ``right`` hand and the ``1`` person with only ``left`` hand images.
-
-Data are divided as follows (the number means original persons ``ID`` (as in
-data collection)):
-
-1) ``dev`` data - [1, 3, 5, 6, 12, 15, 22, 23, 25, 45, 69, 71, 74, 76, 77, 78, 84, 129, 132, 134]
-2) ``eval`` data - [4, 7, 21, 42, 43, 48, 54, 57, 58, 72, 73, 75, 83, 90, 99, 130, 131, 138, 141, 143]
-3) ``world`` data - [13, 14, 17, 20, 24, 28, 31, 39, 51, 60, 68, 128, 133] + [37] + [2, 11, 46, 70]
-
-In the ``enroll`` data sets are images only from session ``1`` whereas in
-``probe`` data sets -- session's ``2`` and ``3`` data.
-
-
-Protocols
-#########
-
-There currently are 6 *standard* protocols:
-
-- ``Idiap_1_1_R``
-- ``Idiap_1_5_R``
-- ``Idiap_5_5_R``
-- ``Idiap_1_1_L``
-- ``Idiap_1_5_L``
-- ``Idiap_5_5_L``
-
-The general form::
-
- Idiap_<a>_<b>_<c>
-
-* a -- number of attempts used to construct model;
-* b -- number of attempt images used to construct model;
-* c -- hand (``L`` or ``R``). Always all images are used, the opposite hand's images are mirrored.
-
-E.g. in protocol ``Idiap_5_5_R`` per one hand only one enroll model is
-constructed using all session ``1`` images (``5 attempt x 5 images``). In this
-protocol ``right`` hands are included unchanged, but ``left`` hands are
-mirrored.
-
-After data alignment were annotated, that included common point finding between
-each person images, we noted that some of the person data were almost impossible
-to annotate. Hands were:
-
-- Person_002/Right
-- Person_005/Left
-- Person_015/Right
-- Person_046/Right
-- Person_068/Right
-- Person_068/Left
-- Person_129/Right
-- Person_138/Left
-
-For protocols:
-
-- ``Idiap_1_1_R_less``
-- ``Idiap_1_5_R_less``
-- ``Idiap_5_5_R_less``
-
-also listed hand data were removed.
-
-
-Protocol ``Idiap_3_5_R`` is not *standard* - in this protocol enroll model is
-constructed using all 3 session 1st attempt images (thus each model consists of
-``3x5=15`` images). This protocol is made to understand the enroll image
-variabilities impact on the recognition rate.
-
-Finally, the protocols:
-
-- ``Idiap_1_1_R_BEAT_test``
-- ``Idiap_1_5_R_BEAT_test``
-- ``Idiap_5_5_R_BEAT_test``
-
-are made as test protocols mainly for the BEAT platform. Again, the numbers in
-the name indicates number of images per attempt and attempt count per each
-enroll model. Each of the protocol groups consists of only 2 person data:
-
-- train -- [128, 133],
-- dev -- [132, 134],
-- eval -- [141, 143].
-
-All these protocols uses the ``advanced_vein_recognition_2`` template.
-
-Annotations
-###########
-
-
-8% of database files have annotations (2 images per session, 6 images per hand,
-altogether 666 images). There are:
-
-- vein pattern binary annotations;
-- ROI binary annotations;
-- alignment point annotations (for each hand 3-5 points marked).
-
-
-Annotations to replace extractors
-#################################
-
-
-Special protocols that consists only the files that have annotations are made.
-Meaning, these protocols can be used to run !!!!! TBD
-
-
-
-
-
-The organisation of the database is the same as before, only now, because there
-are only 2 annotated images per session, protocols are renamed accordingly (also
-note, that now protocols ``Idiap_1_5_R`` and ``Idiap_1_5_L`` doesn't make any
-sense and are removed, because there are only 1 image per attempt that is
-annotated):
-
-- ``Idiap_1_1_R`` -> renamed as ``Idiap_1_1_R_annotations``;
-- ``Idiap_5_5_R`` -> renamed as ``Idiap_2_1_R_annotations``;
-- ``Idiap_1_1_L`` -> renamed as ``Idiap_1_1_L_annotations``;
-- ``Idiap_5_5_L`` -> renamed as ``Idiap_2_1_L_annotations``;
-
-
-Also, the same as ``Idiap_<a>_<b>_<c>_BEAT_test`` protocols were created to
-speedy test BEAT implementation and compare results with ``bob.bio.vein``, also
-test protocols for annotations are implemented:
-
-- ``Idiap_1_1_R_annotations_BEAT_test``;
-- ``Idiap_2_1_R_annotations_BEAT_test``;
-- ``Idiap_1_1_L_annotations_BEAT_test``;
-- ``Idiap_2_1_L_annotations_BEAT_test``;
-
-These protocols uses the ``advanced_vein_annotations`` template.
-
-Also, to benchmark different algorithms against **all** image annotations, there
-are implemented protocol ``annotations_benchmark`` that is implemented using
-``advanced_annotation_benchmark`` template.
-
diff --git a/system/dataformats/system_username/array_1d_coordinates/1.json b/system/dataformats/system_username/array_1d_coordinates/1.json
new file mode 100644
index 0000000..6e08869
--- /dev/null
+++ b/system/dataformats/system_username/array_1d_coordinates/1.json
@@ -0,0 +1,7 @@
+{
+ "#description": "One-dimensional array of 2D integer coordinates",
+ "value": [
+ 0,
+ "{{ system_user.username }}/coordinates/1"
+ ]
+}
--
GitLab