From d5d1d787ca8c014edc48a64f14b0e40ce11dea73 Mon Sep 17 00:00:00 2001
From: Amir MOHAMMADI <amir.mohammadi@idiap.ch>
Date: Thu, 6 Jun 2019 15:24:45 +0200
Subject: [PATCH] Adds a sort command and small fixes
---
bob/bio/base/annotator/FailSafe.py | 2 ++
bob/bio/base/grid.py | 3 +-
bob/bio/base/script/sort.py | 36 +++++++++++++++++++++++
bob/bio/base/test/test_commands.py | 46 +++++++++++++++++++++++-------
bob/bio/base/utils/io.py | 5 +++-
conda/meta.yaml | 1 +
setup.py | 1 +
7 files changed, 82 insertions(+), 12 deletions(-)
create mode 100644 bob/bio/base/script/sort.py
diff --git a/bob/bio/base/annotator/FailSafe.py b/bob/bio/base/annotator/FailSafe.py
index bfad2513..b690f243 100644
--- a/bob/bio/base/annotator/FailSafe.py
+++ b/bob/bio/base/annotator/FailSafe.py
@@ -48,6 +48,8 @@ class FailSafe(Annotator):
if not annotations:
logger.debug(
"Annotator `%s' returned empty annotations.", annotator)
+ else:
+ logger.debug("Annotator `%s' succeeded!", annotator)
kwargs['annotations'].update(annotations or {})
# check if we have all the required annotations
if all(key in kwargs['annotations'] for key in self.required_keys):
diff --git a/bob/bio/base/grid.py b/bob/bio/base/grid.py
index 60aa0125..791604d0 100644
--- a/bob/bio/base/grid.py
+++ b/bob/bio/base/grid.py
@@ -8,13 +8,14 @@ PREDEFINED_QUEUES = {
'default' : {},
'2G' : {'queue' : 'all.q', 'memfree' : '2G'},
'4G' : {'queue' : 'all.q', 'memfree' : '4G'},
+ '4G-q1d' : {'queue' : 'q1d', 'memfree' : '4G'},
'4G-io-big' : {'queue' : 'q1d', 'memfree' : '4G', 'io_big' : True},
'8G' : {'queue' : 'q1d', 'memfree' : '8G'},
'8G-io-big' : {'queue' : 'q1d', 'memfree' : '8G', 'io_big' : True},
'16G' : {'queue' : 'q1dm', 'memfree' : '16G', 'pe_opt' : 'pe_mth 2', 'hvmem' : '8G'},
'16G-io-big' : {'queue' : 'q1dm', 'memfree' : '16G', 'pe_opt' : 'pe_mth 2', 'hvmem' : '8G', 'io_big' : True},
'32G' : {'queue' : 'q1dm', 'memfree' : '32G', 'pe_opt' : 'pe_mth 4', 'hvmem' : '8G', 'io_big' : True},
- '64G' : {'queue' : 'q1dm', 'memfree' : '64G', 'pe_opt' : 'pe_mth 8', 'hvmem' : '8G', 'io_big' : True},
+ '64G' : {'queue' : 'q1dm', 'memfree' : '56G', 'pe_opt' : 'pe_mth 8', 'hvmem' : '7G', 'io_big' : True},
'Week' : {'queue' : 'q1wm', 'memfree' : '32G', 'pe_opt' : 'pe_mth 4', 'hvmem' : '8G'},
'GPU' : {'queue' : 'gpu'}
}
diff --git a/bob/bio/base/script/sort.py b/bob/bio/base/script/sort.py
new file mode 100644
index 00000000..74691263
--- /dev/null
+++ b/bob/bio/base/script/sort.py
@@ -0,0 +1,36 @@
+"""Sorts score files based on their score value
+"""
+import click
+import logging
+import numpy
+from bob.bio.base.score.load import load_score, dump_score
+from bob.extension.scripts.click_helper import verbosity_option, log_parameters
+
+logger = logging.getLogger(__name__)
+
+
+@click.command(
+ epilog="""\b
+Examples:
+
+ $ bob bio sort -vvv /path/to/scores
+"""
+)
+@click.argument(
+ "score_paths",
+ type=click.Path(exists=True, file_okay=True, dir_okay=False, writable=True),
+ nargs=-1,
+)
+@verbosity_option()
+def sort(score_paths, **kwargs):
+ """Sorts score files based on their score values
+
+ The conversion happens in-place; backup your scores before using this script
+ """
+ log_parameters(logger)
+
+ for path in score_paths:
+ logger.info("Sorting: %s", path)
+ scores = load_score(path)
+ scores = scores[numpy.argsort(scores["score"])]
+ dump_score(path, scores)
diff --git a/bob/bio/base/test/test_commands.py b/bob/bio/base/test/test_commands.py
index 8a92e486..dbe1ace1 100644
--- a/bob/bio/base/test/test_commands.py
+++ b/bob/bio/base/test/test_commands.py
@@ -1,12 +1,14 @@
'''Tests for bob.measure scripts'''
-import sys
-import filecmp
import click
from click.testing import CliRunner
+import shutil
import pkg_resources
-from ..script import commands
+import numpy
+import nose
from bob.extension.scripts.click_helper import assert_click_runner_result
+from ..script import commands, sort
+from ..score import scores
def test_metrics():
dev1 = pkg_resources.resource_filename('bob.bio.base.test',
@@ -87,7 +89,6 @@ def test_metrics():
assert_click_runner_result(result)
-
def test_roc():
dev1 = pkg_resources.resource_filename('bob.bio.base.test',
'data/dev-4col.txt')
@@ -138,7 +139,6 @@ def test_roc():
assert_click_runner_result(result)
-
def test_det():
dev1 = pkg_resources.resource_filename('bob.bio.base.test',
'data/dev-4col.txt')
@@ -170,7 +170,6 @@ def test_det():
click.echo(result.output)
assert_click_runner_result(result)
-
dev_nonorm = pkg_resources.resource_filename('bob.bio.base.test',
'data/scores-nonorm-dev')
dev_ztnorm = pkg_resources.resource_filename('bob.bio.base.test',
@@ -225,7 +224,6 @@ def test_epc():
assert_click_runner_result(result)
-
def test_hist():
dev1 = pkg_resources.resource_filename('bob.bio.base.test',
'data/dev-4col.txt')
@@ -260,7 +258,6 @@ def test_hist():
assert_click_runner_result(result)
-
def test_cmc():
dev1 = pkg_resources.resource_filename('bob.bio.base.test',
'data/scores-cmc-5col.txt')
@@ -296,8 +293,6 @@ def test_cmc():
assert_click_runner_result(result)
-
-
def test_dir():
dev1 = pkg_resources.resource_filename('bob.bio.base.test',
'data/scores-nonorm-openset-dev')
@@ -317,3 +312,34 @@ def test_dir():
if result.output:
click.echo(result.output)
assert_click_runner_result(result)
+
+
+def test_sort():
+
+ def sorted_scores(score_lines):
+ lines = []
+ floats = []
+ for line in score_lines:
+ lines.append(line)
+ floats.append(line[-1])
+ sort_idx = numpy.argsort(floats)
+ lines = [lines[i] for i in sort_idx]
+ return lines
+
+ dev1 = pkg_resources.resource_filename('bob.bio.base.test',
+ 'data/scores-nonorm-dev')
+ runner = CliRunner()
+ with runner.isolated_filesystem():
+ # create a temporary sort file and sort it and check if it is sorted!
+
+ path = "scores.txt"
+ shutil.copy(dev1, path)
+
+ result = runner.invoke(sort.sort, [path])
+ assert_click_runner_result(result, exit_code=0)
+
+ # load dev1 and sort it and compare to path
+ dev1_sorted = sorted_scores(scores(dev1))
+ path_scores = list(scores(path))
+
+ nose.tools.assert_list_equal(dev1_sorted, path_scores)
diff --git a/bob/bio/base/utils/io.py b/bob/bio/base/utils/io.py
index e9f6424f..d69fece9 100644
--- a/bob/bio/base/utils/io.py
+++ b/bob/bio/base/utils/io.py
@@ -306,7 +306,10 @@ def vstack_features(reader, paths, same_size=False, allow_missing_files=False):
raise ValueError("Both same_size and allow_missing_files cannot be True at"
" the same time.")
iterable = _generate_features(reader, paths, same_size, allow_missing_files)
- dtype, shape = next(iterable)
+ try:
+ dtype, shape = next(iterable)
+ except StopIteration:
+ return numpy.array([])
if same_size:
total_size = int(len(paths) * numpy.prod(shape))
all_features = numpy.fromiter(iterable, dtype, total_size)
diff --git a/conda/meta.yaml b/conda/meta.yaml
index 1287a68b..ecea2f8f 100644
--- a/conda/meta.yaml
+++ b/conda/meta.yaml
@@ -75,6 +75,7 @@ test:
- bob bio dir --help
- bob bio gen --help
- bob bio evaluate --help
+ - bob bio sort --help
- nosetests --with-coverage --cover-package={{ name }} -sv {{ name }}
- sphinx-build -aEW {{ project_dir }}/doc {{ project_dir }}/sphinx
- sphinx-build -aEb doctest {{ project_dir }}/doc sphinx
diff --git a/setup.py b/setup.py
index 0fb586ed..d8d2797c 100644
--- a/setup.py
+++ b/setup.py
@@ -149,6 +149,7 @@ setup(
'gen = bob.bio.base.script.gen:gen',
'evaluate = bob.bio.base.script.commands:evaluate',
'baseline = bob.bio.base.script.baseline:baseline',
+ 'sort = bob.bio.base.script.sort:sort',
],
# annotators
--
GitLab