def test_02_01_run_headless(self):
output_directory = tempfile.mkdtemp()
temp_directory = os.path.join(output_directory, "temp")
os.mkdir(temp_directory)
try:
#
# Run with a .cp file
#
input_directory = maybe_download_example_images(["ExampleHT29"], [
'AS_09125_050116030001_D03f00d0.tif',
'AS_09125_050116030001_D03f00d1.tif',
'AS_09125_050116030001_D03f00d2.tif', 'ExampleHT29.cp',
'k27IllumCorrControlv1.mat'
])
pipeline_file = os.path.join(input_directory, "ExampleHT29.cp")
measurements_file = os.path.join(output_directory,
"Measurements.h5")
done_file = os.path.join(output_directory, "Done.txt")
self.run_cellprofiler("-c", "-r", "-i", input_directory, "-o",
output_directory, "-p", pipeline_file, "-d",
done_file, "-t", temp_directory,
measurements_file)
import cellprofiler.preferences as cpprefs
self.assertTrue(os.path.exists(measurements_file))
self.assertTrue(os.path.exists(done_file))
#
# Re-run using the measurements file.
#
m2_file = os.path.join(output_directory, "M2.h5")
self.run_cellprofiler("-c", "-r", "-i", input_directory, "-o",
output_directory, "-p", measurements_file,
m2_file)
self.assertTrue(os.path.exists(m2_file))
finally:
shutil.rmtree(output_directory)
def test_02_02_scale(self):
'''Load an image twice, as scaled and unscaled'''
folder = "ExampleSpecklesImages"
file_names = ["1-162hrh2ax2.tif", "1-162hrh2ax2.tif"]
path = maybe_download_example_images([folder], file_names)
cpprefs.set_default_image_directory(path)
workspace, module = self.make_workspace(file_names)
self.assertTrue(isinstance(module, L.LoadSingleImage))
module.file_settings[0].rescale.value = False
module.file_settings[1].rescale.value = True
module.prepare_run(workspace)
module.run(workspace)
unscaled, scaled = [workspace.image_set.get_image(self.get_image_name(i)).pixel_data
for i in range(2)]
np.testing.assert_almost_equal(unscaled * 65535. / 4095., scaled)
def test_02_02_scale(self):
'''Load an image twice, as scaled and unscaled'''
folder = "ExampleSpecklesImages"
file_names = ["1-162hrh2ax2.tif", "1-162hrh2ax2.tif"]
path = maybe_download_example_images([folder], file_names)
cpprefs.set_default_image_directory(path)
workspace, module = self.make_workspace(file_names)
self.assertTrue(isinstance(module, L.LoadSingleImage))
module.file_settings[0].rescale.value = False
module.file_settings[1].rescale.value = True
module.prepare_run(workspace)
module.run(workspace)
unscaled, scaled = [
workspace.image_set.get_image(self.get_image_name(i)).pixel_data
for i in range(2)
]
np.testing.assert_almost_equal(unscaled * 65535. / 4095., scaled)
def test_02_01_run_headless(self):
output_directory = tempfile.mkdtemp()
temp_directory = os.path.join(output_directory, "temp")
os.mkdir(temp_directory)
try:
#
# Run with a .cp file
#
input_directory = maybe_download_example_images(
["ExampleHT29"],
['AS_09125_050116030001_D03f00d0.tif',
'AS_09125_050116030001_D03f00d1.tif',
'AS_09125_050116030001_D03f00d2.tif',
'ExampleHT29.cp', 'k27IllumCorrControlv1.mat'])
pipeline_file = os.path.join(input_directory, "ExampleHT29.cp")
measurements_file = os.path.join(output_directory, "Measurements.h5")
done_file = os.path.join(output_directory, "Done.txt")
self.run_cellprofiler("-c", "-r",
"-i", input_directory,
"-o", output_directory,
"-p", pipeline_file,
"-d", done_file,
"-t", temp_directory,
measurements_file)
import cellprofiler.preferences as cpprefs
self.assertTrue(os.path.exists(measurements_file))
self.assertTrue(os.path.exists(done_file))
#
# Re-run using the measurements file.
#
m2_file = os.path.join(output_directory, "M2.h5")
self.run_cellprofiler("-c", "-r",
"-i", input_directory,
"-o", output_directory,
"-p", measurements_file,
m2_file)
self.assertTrue(os.path.exists(m2_file))
finally:
shutil.rmtree(output_directory)
