def test_13_01_load_filename(self):
#
# Load a file, only specifying the FileName in the CSV
#
dir = os.path.join(example_images_directory(), "ExampleSBSImages")
file_name = 'Channel2-01-A-01.tif'
csv_text = '''"Image_FileName_DNA"
"%s"
'''% file_name
pipeline, module, filename = self.make_pipeline(csv_text)
assert isinstance(module, L.LoadData)
module.image_directory.dir_choice = cps.ABSOLUTE_FOLDER_NAME
module.image_directory.custom_path = dir
m = cpmeas.Measurements(mode="memory")
workspace = cpw.Workspace(pipeline, module, m, cpo.ObjectSet(),
m, cpi.ImageSetList())
self.assertTrue(module.prepare_run(workspace))
self.assertEqual(m.get_measurement(cpmeas.IMAGE, "FileName_DNA", 1),
file_name)
path = m.get_measurement(cpmeas.IMAGE, "PathName_DNA", 1)
self.assertEqual(path, dir)
self.assertEqual(m.get_measurement(cpmeas.IMAGE, "URL_DNA", 1),
L.pathname2url(os.path.join(dir, file_name)))
module.prepare_group(workspace, {}, [1])
module.run(workspace)
img = workspace.image_set.get_image("DNA", must_be_grayscale=True)
self.assertEqual(tuple(img.pixel_data.shape), (640, 640))
def test_13_01_load_filename(self):
#
# Load a file, only specifying the FileName in the CSV
#
dir = os.path.join(example_images_directory(), "ExampleSBSImages")
file_name = 'Channel2-01-A-01.tif'
csv_text = '''"Image_FileName_DNA"
"%s"
''' % file_name
pipeline, module, filename = self.make_pipeline(csv_text)
assert isinstance(module, L.LoadData)
module.image_directory.dir_choice = cps.ABSOLUTE_FOLDER_NAME
module.image_directory.custom_path = dir
m = cpmeas.Measurements(mode="memory")
workspace = cpw.Workspace(pipeline, module, m, cpo.ObjectSet(), m,
cpi.ImageSetList())
self.assertTrue(module.prepare_run(workspace))
self.assertEqual(m.get_measurement(cpmeas.IMAGE, "FileName_DNA", 1),
file_name)
path = m.get_measurement(cpmeas.IMAGE, "PathName_DNA", 1)
self.assertEqual(path, dir)
self.assertEqual(m.get_measurement(cpmeas.IMAGE, "URL_DNA", 1),
L.pathname2url(os.path.join(dir, file_name)))
module.prepare_group(workspace, {}, [1])
module.run(workspace)
img = workspace.image_set.get_image("DNA", must_be_grayscale=True)
self.assertEqual(tuple(img.pixel_data.shape), (640, 640))
def test_13_06_load_default_input_folder(self):
# Regression test of issue #1365 - load a file from the default
# input folder and check that PathName_xxx is absolute
csv_text = '''"Image_FileName_DNA","Image_PathName_DNA"\n"%s","%s"''' \
% (self.test_filename, self.test_path)
pipeline, module, filename = self.make_pipeline(csv_text)
try:
assert isinstance(module, L.LoadData)
module.image_directory.dir_choice = cps.ABSOLUTE_FOLDER_NAME
module.image_directory.custom_path = self.test_path
m = cpmeas.Measurements()
workspace = cpw.Workspace(pipeline, module, m, cpo.ObjectSet(),
m, cpi.ImageSetList())
self.assertTrue(module.prepare_run(workspace))
self.assertEqual(m.get_measurement(cpmeas.IMAGE, "FileName_DNA", 1),
self.test_filename)
path_out = m.get_measurement(cpmeas.IMAGE, "PathName_DNA", 1)
self.assertEqual(self.test_path, path_out)
self.assertEqual(
m.get_measurement(cpmeas.IMAGE, "URL_DNA", 1),
L.pathname2url(os.path.join(self.test_path, self.test_filename)))
module.prepare_group(workspace, {}, [1])
module.run(workspace)
img = workspace.image_set.get_image("DNA", must_be_grayscale=True)
self.assertEqual(tuple(img.pixel_data.shape), self.test_shape)
finally:
os.remove(filename)
def test_13_06_load_default_input_folder(self):
# Regression test of issue #1365 - load a file from the default
# input folder and check that PathName_xxx is absolute
csv_text = '''"Image_FileName_DNA","Image_PathName_DNA"\n"%s","%s"''' \
% (self.test_filename, self.test_path)
pipeline, module, filename = self.make_pipeline(csv_text)
try:
assert isinstance(module, L.LoadData)
module.image_directory.dir_choice = cps.ABSOLUTE_FOLDER_NAME
module.image_directory.custom_path = self.test_path
m = cpmeas.Measurements()
workspace = cpw.Workspace(pipeline, module, m, cpo.ObjectSet(), m,
cpi.ImageSetList())
self.assertTrue(module.prepare_run(workspace))
self.assertEqual(
m.get_measurement(cpmeas.IMAGE, "FileName_DNA", 1),
self.test_filename)
path_out = m.get_measurement(cpmeas.IMAGE, "PathName_DNA", 1)
self.assertEqual(self.test_path, path_out)
self.assertEqual(
m.get_measurement(cpmeas.IMAGE, "URL_DNA", 1),
L.pathname2url(os.path.join(self.test_path,
self.test_filename)))
module.prepare_group(workspace, {}, [1])
module.run(workspace)
img = workspace.image_set.get_image("DNA", must_be_grayscale=True)
self.assertEqual(tuple(img.pixel_data.shape), self.test_shape)
finally:
os.remove(filename)
