def test_submatrix(self):
"""crop"""
tempdir = mkdtemp()
# crop the test image (size=1388x1040) to be bottom right tile of the test image
# tiled with 6 cols and 5 rows => ROI= 231x208+1155+832
orig_big = join(
pychrm_test_dir,
'lymphoma_eosin_channel_MCL_test_img_sj-05-3362-R2_001_E.tif')
orig_cropped = join(
pychrm_test_dir,
'lymphoma_eosin_channel_MCL_test_img_sj-05-3362-R2_001_E-t6x5_5_4-l.tiff'
)
test_cropped_path = join(tempdir, 'TEST_submatrix.tif')
x = 1155
y = 832
w = 231
h = 208
x1 = x
y1 = y
x2 = x1 + w - 1
y2 = y1 + h - 1
# setting mean = 0 is flag to not use mean in ImageMatrix::OpenImage()
downsample = 0
bb = None
mean = 0.0
stddev = 0.0
try:
origim = PyImageMatrix()
if 1 != origim.OpenImage(orig_big, downsample, bb, mean, stddev):
self.fail('Could not build an ImageMatrix from ' + orig_big)
# API calls for copying desired pixels into empty ImageMatrix instance:
# the_tiff is garbage collected on return
cropped_im = PyImageMatrix()
# void ImageMatrix::submatrix (const ImageMatrix &matrix, const unsigned int x1, const unsigned int y1, const unsigned int x2, const unsigned int y2)
cropped_im.submatrix(origim, x1, y1, x2, y2) # no retval
cropped_im.SaveTiff(test_cropped_path)
orig_pixels = plt.imread(orig_cropped)
cropped_pixels = plt.imread(test_cropped_path)
assert_equal(orig_pixels, cropped_pixels)
finally:
rmtree(tempdir)
def test_submatrix(self):
"""crop"""
tempdir = mkdtemp()
# crop the test image (size=1388x1040) to be bottom right tile of the test image
# tiled with 6 cols and 5 rows => ROI= 231x208+1155+832
orig_big = join(
pychrm_test_dir,
'lymphoma_eosin_channel_MCL_test_img_sj-05-3362-R2_001_E.tif')
orig_cropped = join(
pychrm_test_dir,
'lymphoma_eosin_channel_MCL_test_img_sj-05-3362-R2_001_E-t6x5_5_4-l.tiff'
)
test_cropped_path = join(tempdir, 'TEST_submatrix.tif')
x = 1155
y = 832
w = 231
h = 208
x1 = x
y1 = y
x2 = x1 + w - 1
y2 = y1 + h - 1
# setting mean = 0 is flag to not use mean in ImageMatrix::OpenImage()
downsample = 0
bb = None
mean = 0.0
stddev = 0.0
try:
origim = PyImageMatrix()
if 1 != origim.OpenImage(orig_big, downsample, bb, mean, stddev):
self.fail('Could not build an ImageMatrix from ' + orig_big)
# API calls for copying desired pixels into empty ImageMatrix instance:
# the_tiff is garbage collected on return
cropped_im = PyImageMatrix()
# void ImageMatrix::submatrix (const ImageMatrix &matrix, const unsigned int x1, const unsigned int y1, const unsigned int x2, const unsigned int y2)
cropped_im.submatrix(origim, x1, y1, x2, y2) # no retval
cropped_im.SaveTiff(test_cropped_path)
orig_pixels = plt.imread(orig_cropped)
cropped_pixels = plt.imread(test_cropped_path)
assert_equal(orig_pixels, cropped_pixels)
finally:
rmtree(tempdir)
