def test_SaveImage(self):
"""SaveImage pixels to file."""
tempdir = mkdtemp()
orig = join(
pychrm_test_dir,
'lymphoma_eosin_channel_MCL_test_img_sj-05-3362-R2_001_E.tif')
# 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, downsample, bb, mean, stddev):
self.fail('Could not build an ImageMatrix from ' + orig)
copied_tiff = join(tempdir, 'TEST1.tif')
origim.SaveTiff(copied_tiff)
orig_pixels = plt.imread(orig)
copied_pixels = plt.imread(copied_tiff)
assert_equal(orig_pixels, copied_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)
def test_OpenImage(self):
"""Testing ROI open functionality"""
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_OpenImageROI.tif')
x = 1155
y = 832
w = 231
h = 208
from wndcharm import rect
bb = rect()
bb.x = x
bb.y = y
bb.w = w
bb.h = h
# setting mean = 0 is flag to not use mean in ImageMatrix::OpenImage()
downsample = 0
#bb = None
mean = 0.0
stddev = 0.0
try:
cropped_on_load_im = PyImageMatrix()
if 1 != cropped_on_load_im.OpenImage(orig_big, downsample, bb,
mean, stddev):
self.fail('Could not build an ImageMatrix from ' + orig_big)
cropped_on_load_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_allocate(self):
"""make an empty pixel plane"""
tempdir = mkdtemp()
test_path = join(tempdir, "TEST_allocate.tif")
num_rows, num_cols = shape = (123, 456)
try:
origim = PyImageMatrix()
# virtual void allocate (unsigned int w, unsigned int h);
origim.allocate(num_cols, num_rows)
origim.SaveTiff(test_path)
pixels = plt.imread(test_path)
self.assertEqual(pixels.shape, shape)
finally:
rmtree(tempdir)