def setUpClass(cls):
maybe_download_sbs()
cls.test_folder = "loaddata"
cls.test_path = os.path.join(
example_images_directory(), cls.test_folder)
cls.test_filename = "image.tif"
cls.test_shape = (13, 15)
path = maybe_download_example_image([cls.test_folder],
cls.test_filename,
shape=cls.test_shape)
with open(path, "rb") as fd:
cls.test_md5 = hashlib.md5(fd.read()).hexdigest()
def setUpClass(cls):
maybe_download_sbs()
cls.test_folder = "loaddata"
cls.test_path = os.path.join(
example_images_directory(), cls.test_folder)
cls.test_filename = "image.tif"
cls.test_shape = (13, 15)
path = maybe_download_example_image([cls.test_folder],
cls.test_filename,
shape=cls.test_shape)
with open(path, "rb") as fd:
cls.test_md5 = hashlib.md5(fd.read()).hexdigest()
def test_03_01_save_and_load(self):
"""Save a pipeline to batch data, open it to check and load it"""
data = ("eJztWW1PGkEQXhC1WtPYTzb9tB+llROoGiWNgi9NSYUSIbZGbbvCApvu7ZJ7"
"UWlj0o/9Wf1J/QndxTs4tsoBRS3JHbkcMzfPPDOzs8uxl8uU9jPbcFWLw1ym"
"FKsSimGBIqvKDT0FmbUEdwyMLFyBnKVgycYwY9dgIgET8dTqRmolCZPx+AYY"
"7ghlc0/EJf4cgClxfSTOsHNr0pFDnlPKRWxZhNXMSRABzxz9L3EeIoOgM4oP"
"EbWx2aFw9VlW5aVmo30rxys2xXmke43Fkbf1M2yY76su0LldIJeYFsk3rKTg"
"mh3gc2ISzhy841/Vtnm5pfDKOhTmOnUIKXWQdVnw6KX9W9Cxj9xQt6ce+3lH"
"JqxCzknFRhQSHdXaUbTGwcffRJe/CXAk0BKX9sHNK3HIs4QvrdjeJSpbUEdW"
"uS79rPv4mVb8SLmcOrGw3ugr/lAXPgRe9Zl3uAsXBnkO+sp7VolXyrscMm5B"
"28T91/02/lHgphSce7i4GdCJ0y/fOSVfKe9RE1/UsYE1TXP91H38rCh+pCzG"
"uYwpbRhcLlHGiWXY7OuJaCC9ISZ3q5NdqbhdzLZb+yH4hpmXy3I2ioVtGTFE"
"myYZxbwcdpzvu68eku8+cGmf/GZAdz9IeaeOGMM0ERtx3P30z24+c6d86jqc"
"uOP8Il18EdE/DP8L3w8fvnegezyl/Glxq/BaPljhTe1l9LOUPoj15YBfbB5n"
"YoXTqKvZ4dTW2eZxPLZx+j2xlLy6Ni4SgWwpozfmPUj8fuvhuhK/lGUMRxgZ"
"TmArV9GYVOU4s+qOLunodlGzo3mgeZMcxbwZir9p8QZFpj4C/kHnUfKO+YJ5"
"NJ7z6OPsYP8rxuV3NcAFuAAX4P43XNqD63c/pLUZUzO43YCEVXBjnPINcOON"
"S4OgXwPc8DipvO35Ut2/kfZfQO9+ewG6+03K3s04TW9topsa5ahyvYut7Yuv"
"Wc+Gdj/P52sKz9ptPOXWK5AzuU8tb5ja9TuRbal4Q1rvCNT6zdzA561DWHwW"
"pnvXXa13Zxx+bw3DFwn9zffYBxdxKidxP8Fg47zYw97NbVj7P/nFW+E=")
def callback(caller, event):
self.assertFalse(isinstance(event, cpp.LoadExceptionEvent))
self.assertFalse(isinstance(event, cpp.RunExceptionEvent))
T.maybe_download_sbs()
for windows_mode in ((False,
True) if sys.platform.startswith("win") else
(False, )):
pipeline = cpp.Pipeline()
pipeline.add_listener(callback)
pipeline.load(StringIO(zlib.decompress(base64.b64decode(data))))
ipath = os.path.join(T.example_images_directory(),
"ExampleSBSImages")
bpath = tempfile.mkdtemp()
bfile = os.path.join(bpath, C.F_BATCH_DATA)
hfile = os.path.join(bpath, C.F_BATCH_DATA_H5)
try:
li = pipeline.modules()[0]
self.assertTrue(isinstance(li, LI.LoadImages))
module = pipeline.modules()[1]
self.assertTrue(isinstance(module, C.CreateBatchFiles))
li.location.dir_choice = cps.ABSOLUTE_FOLDER_NAME
li.location.custom_path = ipath
module.wants_default_output_directory.value = False
module.custom_output_directory.value = bpath
module.remote_host_is_windows.value = windows_mode
self.assertEqual(len(module.mappings), 1)
mapping = module.mappings[0]
mapping.local_directory.value = ipath
self.assertFalse(pipeline.in_batch_mode())
measurements = cpmeas.Measurements(mode="memory")
image_set_list = cpi.ImageSetList()
result = pipeline.prepare_run(
cpw.Workspace(pipeline, None, None, None, measurements,
image_set_list))
self.assertFalse(pipeline.in_batch_mode())
self.assertFalse(result)
self.assertFalse(module.batch_mode.value)
self.assertTrue(
measurements.has_feature(cpmeas.EXPERIMENT,
cpp.M_PIPELINE))
pipeline = cpp.Pipeline()
pipeline.add_listener(callback)
image_set_list = cpi.ImageSetList()
measurements = cpmeas.Measurements(mode="memory")
workspace = cpw.Workspace(pipeline, None, None, None,
cpmeas.Measurements(),
image_set_list)
workspace.load(hfile, True)
measurements = workspace.measurements
self.assertTrue(pipeline.in_batch_mode())
module = pipeline.modules()[1]
self.assertTrue(isinstance(module, C.CreateBatchFiles))
self.assertTrue(module.batch_mode.value)
image_numbers = measurements.get_image_numbers()
self.assertTrue(
[x == i + 1 for i, x in enumerate(image_numbers)])
pipeline.prepare_run(workspace)
pipeline.prepare_group(workspace, {}, list(range(1, 97)))
for i in range(96):
image_set = image_set_list.get_image_set(i)
for image_name in ("DNA", "Cytoplasm"):
pathname = measurements.get_measurement(
cpmeas.IMAGE, "PathName_" + image_name, i + 1)
self.assertEqual(
pathname,
"\\imaging\\analysis"
if windows_mode else "/imaging/analysis",
)
measurements.close()
finally:
if os.path.exists(bfile):
os.unlink(bfile)
if os.path.exists(hfile):
os.unlink(hfile)
os.rmdir(bpath)
def test_03_01_save_and_load(self):
'''Save a pipeline to batch data, open it to check and load it'''
data = ('eJztWW1PGkEQXhC1WtPYTzb9tB+llROoGiWNgi9NSYUSIbZGbbvCApvu7ZJ7'
'UWlj0o/9Wf1J/QndxTs4tsoBRS3JHbkcMzfPPDOzs8uxl8uU9jPbcFWLw1ym'
'FKsSimGBIqvKDT0FmbUEdwyMLFyBnKVgycYwY9dgIgET8dTqRmolCZPx+AYY'
'7ghlc0/EJf4cgClxfSTOsHNr0pFDnlPKRWxZhNXMSRABzxz9L3EeIoOgM4oP'
'EbWx2aFw9VlW5aVmo30rxys2xXmke43Fkbf1M2yY76su0LldIJeYFsk3rKTg'
'mh3gc2ISzhy841/Vtnm5pfDKOhTmOnUIKXWQdVnw6KX9W9Cxj9xQt6ce+3lH'
'JqxCzknFRhQSHdXaUbTGwcffRJe/CXAk0BKX9sHNK3HIs4QvrdjeJSpbUEdW'
'uS79rPv4mVb8SLmcOrGw3ugr/lAXPgRe9Zl3uAsXBnkO+sp7VolXyrscMm5B'
'28T91/02/lHgphSce7i4GdCJ0y/fOSVfKe9RE1/UsYE1TXP91H38rCh+pCzG'
'uYwpbRhcLlHGiWXY7OuJaCC9ISZ3q5NdqbhdzLZb+yH4hpmXy3I2ioVtGTFE'
'myYZxbwcdpzvu68eku8+cGmf/GZAdz9IeaeOGMM0ERtx3P30z24+c6d86jqc'
'uOP8Il18EdE/DP8L3w8fvnegezyl/Glxq/BaPljhTe1l9LOUPoj15YBfbB5n'
'YoXTqKvZ4dTW2eZxPLZx+j2xlLy6Ni4SgWwpozfmPUj8fuvhuhK/lGUMRxgZ'
'TmArV9GYVOU4s+qOLunodlGzo3mgeZMcxbwZir9p8QZFpj4C/kHnUfKO+YJ5'
'NJ7z6OPsYP8rxuV3NcAFuAAX4P43XNqD63c/pLUZUzO43YCEVXBjnPINcOON'
'S4OgXwPc8DipvO35Ut2/kfZfQO9+ewG6+03K3s04TW9topsa5ahyvYut7Yuv'
'Wc+Gdj/P52sKz9ptPOXWK5AzuU8tb5ja9TuRbal4Q1rvCNT6zdzA561DWHwW'
'pnvXXa13Zxx+bw3DFwn9zffYBxdxKidxP8Fg47zYw97NbVj7P/nFW+E=')
def callback(caller, event):
self.assertFalse(isinstance(event, cpp.LoadExceptionEvent))
self.assertFalse(isinstance(event, cpp.RunExceptionEvent))
T.maybe_download_sbs()
for windows_mode in ((False, True) if sys.platform.startswith("win")
else (False,)):
pipeline = cpp.Pipeline()
pipeline.add_listener(callback)
pipeline.load(StringIO(zlib.decompress(base64.b64decode(data))))
ipath = os.path.join(T.example_images_directory(), 'ExampleSBSImages')
bpath = tempfile.mkdtemp()
bfile = os.path.join(bpath, C.F_BATCH_DATA)
hfile = os.path.join(bpath, C.F_BATCH_DATA_H5)
try:
li = pipeline.modules()[0]
self.assertTrue(isinstance(li, LI.LoadImages))
module = pipeline.modules()[1]
self.assertTrue(isinstance(module, C.CreateBatchFiles))
li.location.dir_choice = LI.ABSOLUTE_FOLDER_NAME
li.location.custom_path = ipath
module.wants_default_output_directory.value = False
module.custom_output_directory.value = bpath
module.remote_host_is_windows.value = windows_mode
self.assertEqual(len(module.mappings), 1)
mapping = module.mappings[0]
mapping.local_directory.value = ipath
self.assertFalse(pipeline.in_batch_mode())
measurements = cpmeas.Measurements(mode="memory")
image_set_list = cpi.ImageSetList()
result = pipeline.prepare_run(
cpw.Workspace(pipeline, None, None, None,
measurements, image_set_list))
self.assertFalse(pipeline.in_batch_mode())
self.assertFalse(result)
self.assertFalse(module.batch_mode.value)
self.assertTrue(measurements.has_feature(
cpmeas.EXPERIMENT, cpp.M_PIPELINE))
pipeline = cpp.Pipeline()
pipeline.add_listener(callback)
image_set_list = cpi.ImageSetList()
measurements = cpmeas.Measurements(mode="memory")
workspace = cpw.Workspace(pipeline, None, None, None,
cpmeas.Measurements(),
image_set_list)
workspace.load(hfile, True)
measurements = workspace.measurements
self.assertTrue(pipeline.in_batch_mode())
module = pipeline.modules()[1]
self.assertTrue(isinstance(module, C.CreateBatchFiles))
self.assertTrue(module.batch_mode.value)
image_numbers = measurements.get_image_numbers()
self.assertTrue([x == i + 1 for i, x in enumerate(image_numbers)])
pipeline.prepare_run(workspace)
pipeline.prepare_group(workspace, {}, range(1, 97))
for i in range(96):
image_set = image_set_list.get_image_set(i)
for image_name in ('DNA', 'Cytoplasm'):
pathname = measurements.get_measurement(
cpmeas.IMAGE, "PathName_" + image_name, i + 1)
self.assertEqual(pathname,
'\\imaging\\analysis' if windows_mode
else '/imaging/analysis')
measurements.close()
finally:
if os.path.exists(bfile):
os.unlink(bfile)
if os.path.exists(hfile):
os.unlink(hfile)
os.rmdir(bpath)
