Merge branch 'improvements' of gitlab.idiap.ch:bob/bob.io.stream into improvements

MANIFEST.in

 include README.rst buildout.cfg COPYING version.txt requirements.txt
-recursive-include doc *.rst *.png *.ico *.txt
\ No newline at end of file
+recursive-include doc *.py *.rst *.png *.ico *.txt
+recursive-include bob/io/stream *.h5 *.png *.json

README.rst

@@ -20,12 +20,6 @@
 
 This package is part of the signal-processing and machine learning toolbox Bob_.
 
-.. todo::
-
-   **Complete the sentence above to include one phrase about your
-   package!  Once this is done, delete this to-do!**
-
-
 Installation
 ------------
 
@@ -45,4 +39,4 @@ development `mailing list`_.
 .. Place your references here:
 .. _bob: https://www.idiap.ch/software/bob
 .. _installation: https://www.idiap.ch/software/bob/install
-.. _mailing list: https://www.idiap.ch/software/bob/discuss
\ No newline at end of file
+.. _mailing list: https://www.idiap.ch/software/bob/discuss

bob/io/stream/stream.py

@@ -435,7 +435,7 @@ class StreamWarp(StreamFilter):
             output.append(transform.warp(   data[c], 
                                             self.warp_transform, 
                                             output_shape=self.output_shape, 
-                                            preserve_range=True))
+                                            preserve_range=True).astype(data.dtype))
         output = np.stack(output)
 
         return output

bob/io/stream/test.py

-import bob.io.stream
-from bob.ip.viewer import View
-import numpy as np
-import bob.io.base
-import bob.io.image
-import cv2 as cv
-
-import pyqtgraph.exporters
-
-###
-
-v = View()
-
-img,plt = v.setImageMatrix(rows=2, cols=5)
-
-def plot(i, row, col):
-	v.setImageData(i, row, col)
-
-###
-
-
-#f = bob.io.stream.StreamFile(	'/Users/david/Desktop/idiap/data/1_01_0004_0000_00_00_000-dceb260e.h5', 
-#								'/Users/david/Desktop/idiap/bob.io.stream/bob/io/stream/config/batl2_idiap_config.json')
-
-f = bob.io.stream.StreamFile(	'/Users/david/Desktop/idiap/data/1_01_0064_0000_00_00_000-b112ebe7.h5', 
-								'/Users/david/Desktop/idiap/bob.io.stream/bob/io/stream/config/batl2_idiap_config.json')
-
-#print('available streams:')
-#for k in f.get_available_streams():
-#	print(k)
-#print()
-
-
-#print('available filters:')
-#for k in color.get_available_filters():
-#	print(k)
-#print()
-
-# define streams
-
-color = f.stream('color')
-depth = f.stream('depth').clean()
-nir_left = f.stream('nir_left_stereo')
-nir_right = f.stream('nir_right_stereo')
-nir_left_735nm = f.stream('nir_left_735nm')
-nir_left_850nm = f.stream('nir_left_850nm')
-nir_left_940nm = f.stream('nir_left_940nm')
-nir_left_1050nm = f.stream('nir_left_1050nm')
-swir_940nm = f.stream('swir_940nm').clean()
-swir_1050nm = f.stream('swir_1050nm').clean()
-swir_1200nm = f.stream('swir_1200nm').clean()
-swir_1300nm = f.stream('swir_1300nm').clean()
-swir_1450nm = f.stream('swir_1450nm').clean()
-swir_1550nm = f.stream('swir_1550nm').clean()
-swir_1650nm = f.stream('swir_1650nm').clean()
-thermal = f.stream('thermal')
-
-
-
-
-
-
-swir_norm = swir_1050nm.normalize().stack(swir_1300nm.normalize()).stack(swir_1550nm.normalize())
-nir = nir_left_940nm.stack(nir_left_850nm).stack(nir_left_735nm)
-nir_norm = nir_left_940nm.normalize().stack(nir_left_850nm.normalize()).stack(nir_left_735nm.normalize())
-
-nir_left_gray = nir_left.to_rgb(mode='gray')
-
-map_3d = nir_left.stereo(nir_right)
-
-rep_color = color.reproject(nir_left, nir_right, map_3d)
-rep_nir_left = nir_left.reproject(nir_left, nir_right, map_3d)
-rep_nir_right = nir_right.reproject(nir_left, nir_right, map_3d)
-#rep_swir = swir.reproject(nir_left, nir_right, map_3d)
-rep_swir_norm = swir_norm.reproject(nir_left, nir_right, map_3d)
-rep_thermal = thermal.normalize().reproject(nir_left, nir_right, map_3d)
-rep_nir = nir.reproject(nir_left, nir_right, map_3d)
-rep_nir_norm = nir_norm.reproject(nir_left, nir_right, map_3d)
-#rep_swir_1300 = swir_1300.normalize().reproject(nir_left, nir_right, map_3d)
-
-warp_depth = depth.warp(nir_left).normalize(tmin=450, tmax=750)
-
-# load
-
-data_map_3d = map_3d[0][:,100:1500,400:1200]
-data_map_3d_dep = data_map_3d[0]
-data_rep_thermal = rep_thermal[0][:,100:1500,400:1200]
-data_rep_nir_left = rep_nir_left[0][:,100:1500,400:1200]
-data_rep_color = rep_color[0][:,100:1500,400:1200]
-data_rep_nir_right = rep_nir_right[0][:,100:1500,400:1200]
-data_rep_swir_norm = rep_swir_norm[0][:,100:1500,400:1200]
-data_rep_nir = rep_nir[0][:,100:1500,400:1200]
-data_rep_nir_norm = rep_nir_norm[0][:,100:1500,400:1200]
-data_depth = warp_depth[0][:,100:1500,400:1200]
-
-print(data_depth.shape, data_depth.dtype)
-print(np.amin(data_depth), np.amax(data_depth))
-
-print('depth', np.amin(depth[0]), np.amax(depth[0]))
-
-#print('swir', np.amin(swir_1050[0]), np.amax(swir_1050[0]))
-#print('swir', np.amin(swir_1300[0]), np.amax(swir_1300[0]))
-#print('swir', np.amin(swir_1550[0]), np.amax(swir_1550[0]))
-
-#tmin = 300.0
-#tmax = 700.0
-#data_depth = (data_depth - tmin)
-#data_depth = (data_depth * 255.0 / float(tmax - tmin)).astype('uint8')
-
-# export
-
-tmin = np.amin(data_map_3d_dep)
-tmax = np.amax(data_map_3d_dep)
-exp_map_depth = (data_map_3d_dep - tmin).astype('float')
-exp_map_depth = (exp_map_depth * 255.0 / float(tmax - tmin)).astype('uint8')
-exp_map_depth= cv.applyColorMap(exp_map_depth, cv.COLORMAP_JET)
-exp_map_depth = np.moveaxis(exp_map_depth, 2, 0)
-
-exp_intel_depth = cv.applyColorMap(data_depth[0], cv.COLORMAP_JET)
-exp_intel_depth = np.moveaxis(exp_intel_depth, 2, 0)
-print('fin', exp_intel_depth.shape)
-
-exp_thermal = data_rep_thermal[0].astype('uint8')
-exp_thermal = cv.applyColorMap(exp_thermal, cv.COLORMAP_JET)
-exp_thermal = np.moveaxis(exp_thermal, 2, 0)
-
-exp_color = np.flip(data_rep_color, axis=0)
-
-
-exp_nir_l = data_rep_nir_left[0]
-tmin = np.amin(exp_nir_l)
-tmax = np.amax(exp_nir_l)
-exp_nir_l = (exp_nir_l - tmin).astype('float')
-exp_nir_l = (exp_nir_l * 255.0 / float(tmax - tmin)).astype('uint8')
-
-exp_nir_r = data_rep_nir_right[0]
-tmin = np.amin(exp_nir_r)
-tmax = np.amax(exp_nir_r)
-exp_nir_r = (exp_nir_r - tmin).astype('float')
-exp_nir_r = (exp_nir_r * 255.0 / float(tmax - tmin)).astype('uint8')
-
-exp_nir_rl = np.stack([exp_nir_l, exp_nir_l/2 + exp_nir_r/2  , exp_nir_r]).astype('uint8')
-
-exp_rep_nir_norm = data_rep_nir_norm.astype('uint8')
-exp_rep_swir_norm = data_rep_swir_norm.astype('uint8')
-
-print(exp_map_depth.shape, exp_color.shape, exp_rep_swir_norm.shape)
-print(exp_intel_depth.shape, exp_rep_nir_norm.shape, exp_thermal.shape)
-
-exp_top = np.concatenate((exp_map_depth, exp_color,  exp_rep_swir_norm), axis=2)
-exp_bot = np.concatenate((exp_intel_depth, exp_rep_nir_norm, exp_thermal), axis=2)
-print(exp_top.shape, exp_bot.shape)
-exp = np.concatenate((exp_top, exp_bot), axis=1)
-
-bob.io.base.save(exp, 'test.png')
-
-
-# plot
-
-plot(data_depth, 0, 0)
-plot(data_map_3d_dep, 1, 0)
-plot(data_rep_thermal, 0, 1)
-plot(data_rep_nir_left, 1, 1)
-plot(data_rep_color, 0, 2)
-plot(data_rep_nir_right, 1, 2)
-#plot(data_rep_swir, 0, 3)
-plot(data_rep_swir_norm, 1, 3)
-plot(data_rep_nir, 0, 4)
-plot(data_rep_nir_norm, 1, 4)
-
-v.resize(1400,1100)
-plt[0][0].autoRange()
-
-v.show()
-
-quit()
-
-

bob/io/stream/test/test.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+
+"""
+Test Units
+"""
+# ==============================================================================
+from bob.io.stream import StreamFile, Stream
+from bob.ip.stereo import StereoParameters
+from bob.ip.stereo.test.test import is_close_enough
+
+from bob.io.base import load
+
+from pkg_resources import resource_filename
+
+import numpy as np
+
+# ==============================================================================
+
+
+def resource_path(relative_path, package="bob.io.stream"):
+    """Wrapper around pkg_resources to get the paths.
+
+    Args:
+        package (str): package name
+        relative_path (str): Location of the resource in the package
+    """
+
+    return resource_filename(package, relative_path)
+
+
+def test_stream():
+    """
+    Test that a few transforms (stereo, reproject, adjust, colormap, select, warp) applied with streams provide a 
+    similar result to saved groundtruth.
+    """
+
+    gt_color = load(resource_path("test/data/reprojection_color.png"))
+    gt_depth = load(resource_path("test/data/reprojection_depth.png"))
+    gt_warp_thermal = load(resource_path("test/data/warp_thermal.png"))
+    gt_warp_swir = load(resource_path("test/data/warp_swir_norm.png"))
+
+    f = StreamFile(
+        resource_path("test/data/input_example.h5"),
+        resource_path("config/idiap_face_streams.json"),
+        resource_path("config/idiap_face_calibration.json", "bob.ip.stereo"),
+    )
+
+    color = f.stream("color")
+    nir_left = Stream("nir_left_stereo").adjust(color)
+    nir_right = f.stream("nir_right_stereo").adjust(color)
+    swir_1050 = f.stream("swir_1050nm")
+    swir_1300 = f.stream("swir_1300nm")
+    swir_1550 = f.stream("swir_1550nm")
+    thermal = f.stream("thermal")
+
+    # reproject operations
+    map_3d = nir_left.stereo(nir_right)
+    depth = map_3d.select(channel=2).colormap(colormap="jet")
+    rep_color = color.reproject(nir_left, nir_right, map_3d)
+    nir_left.set_source(f)
+
+    # warp operations
+    swir_norm = swir_1550.normalize().stack(swir_1300.normalize()).stack(swir_1550.normalize())
+    warp_swir_norm = swir_norm.warp(color)
+    warp_thermal = thermal.normalize().warp(color)
+
+    # these streams have different timestamps before adjust
+    assert swir_1050.timestamps.shape != color.timestamps.shape
+    assert np.allclose(swir_1050.adjust(color).timestamps, color.timestamps)
+
+    # Compare stereo and projection results
+    assert gt_depth.shape == depth[0].shape  # groundtruth correspond to first frame of stream
+    assert gt_color.shape == rep_color[0].shape
+
+    assert is_close_enough(gt_depth, depth[0])
+    assert is_close_enough(gt_color, rep_color[0])
+
+    # Compare warp results
+    assert is_close_enough(warp_swir_norm[0][0], gt_warp_swir)
+    assert is_close_enough(warp_thermal[0][0], gt_warp_thermal)

bob/io/stream/test_indices.py

-import bob.io.stream
-
-import numpy as np
-import bob.io.base
-import bob.io.image
-import cv2 as cv
-
-
-
-
-#f = bob.io.stream.StreamFile(	'/Users/david/Desktop/idiap/data/1_01_0004_0000_00_00_000-dceb260e.h5', 
-#								'/Users/david/Desktop/idiap/bob.io.stream/bob/io/stream/config/batl2_idiap_config.json')
-
-f = bob.io.stream.StreamFile(	'/Users/david/Desktop/idiap/data/1_01_0064_0000_00_00_000-b112ebe7.h5', 
-								'/Users/david/Desktop/idiap/bob.io.stream/bob/io/stream/config/batl2_idiap_config.json')
-
-# define streams
-
-color = f.stream('color')
-swir = f.stream('swir_1050nm')
-swir_adj = swir.adjust(color)
-
-print(color.shape)
-print(swir.shape)
-print(swir_adj.shape)
-
-print(color.timestamps)
-print(swir.timestamps)
-print(swir_adj.timestamps)
-
-x = swir_adj[0:60:4]
\ No newline at end of file

bob/io/stream/test_warp.py

-import bob.io.stream
-from bob.ip.viewer import View
-import numpy as np
-
-###
-
-v = View()
-
-img,plt = v.setImageMatrix(rows=2, cols=5)
-
-def plot(i, row, col):
-	v.setImageData(i, row, col)
-
-###
-
-
-f = bob.io.stream.StreamFile(	'/Users/david/Desktop/idiap/data/1_01_0004_0000_00_00_000-dceb260e.h5', 
-								'/Users/david/Desktop/idiap/bob.io.stream/bob/io/stream/config/batl2_idiap_config.json')
-
-#f = bob.io.stream.StreamFile(	'/Users/david/Desktop/idiap/data/1_01_0064_0000_00_00_000-b112ebe7.h5', 
-#								'/Users/david/Desktop/idiap/bob.io.stream/bob/io/stream/config/batl2_idiap_config.json')
-
-print('available streams:')
-for k in f.get_available_streams():
-	print(k)
-print()
-
-###
-
-color = f.stream('color')
-
-print('available filters:')
-for k in color.get_available_filters():
-	print(k)
-print()
-
-# define pipelines
-
-nir_left = f.stream('nir_left_stereo')
-nir_right = f.stream('nir_right_stereo')
-nir_735 = f.stream('nir_left_735nm')
-nir_850 = f.stream('nir_left_850nm')
-nir_940 = f.stream('nir_left_940nm')
-swir_1050 = f.stream('swir_1050nm')
-swir_1300 = f.stream('swir_1300nm')
-swir_1550 = f.stream('swir_1550nm')
-thermal = f.stream('thermal')
-
-swir = swir_1550.stack(swir_1300).stack(swir_1050) 
-swir_norm = swir_1550.normalize().stack(swir_1300.normalize()).stack(swir_1550.normalize())
-nir = nir_940.stack(nir_850).stack(nir_735)
-nir_norm = nir_940.normalize().stack(nir_850.normalize()).stack(nir_735.normalize())
-
-nir_left_gray = nir_left.to_rgb(mode='gray')
-
-map_3d = nir_left.stereo(nir_right)
-
-warp_map_3d = map_3d.warp(color)
-warp_color = color.warp(color)
-warp_nir_left = nir_left.warp(color)
-warp_nir_right = nir_right.warp(color)
-warp_swir = swir.warp(color)
-warp_swir_norm = swir_norm.warp(color)
-warp_thermal = thermal.normalize().warp(color)
-warp_nir = nir.warp(color)
-warp_nir_norm = nir_norm.warp(color)
-warp_swir_1300 = swir_1300.normalize().warp(color)
-
-warp_nirl = nir_left.warp(color)
-
-# load and plot first frame
-
-
-plot(nir_left[0], 0, 0)
-plot(warp_map_3d[0], 1, 0)
-plot(warp_thermal[0], 0, 1)
-plot(warp_nir_left[0], 1, 1)
-plot(warp_color[0], 0, 2)
-plot(warp_nir_right[0], 1, 2)
-plot(warp_swir[0], 0, 3)
-plot(warp_swir_norm[0], 1, 3)
-plot(warp_nir[0], 0, 4)
-plot(warp_nir_norm[0], 1, 4)
-
-v.show()
-
-

conda/meta.yaml

@@ -30,6 +30,7 @@ requirements:
     - future
     - scikit-image
     - scipy
+    - opencv
     # place your other host dependencies here
   run:
     - python
@@ -39,6 +40,7 @@ requirements:
     - future
     - scikit-image
     - scipy
+    - opencv
     # place other runtime dependencies here (same as requirements.txt)
 
 test:
@@ -64,4 +66,4 @@ about:
   home: https://www.idiap.ch/software/bob/
   license: GNU General Public License v3 (GPLv3)
   license_family: GPL
-  license_file: ../COPYING
\ No newline at end of file
+  license_file: ../COPYING

doc/api.rst

+.. vim: set fileencoding=utf-8 :
+.. Tue 09 Jun 2020 13:16:45 CET
+
+============
+ Python API
+============
+
+Package Documentation
+---------------------
+
+.. automodule:: bob.io.stream

requirements.txt

@@ -5,4 +5,4 @@ bob.ip.stereo
 future
 matplotlib
 scikit-image
-scipy
\ No newline at end of file
+scipy