def test_01_01_html(self):
path = tempfile.mkdtemp()
try:
CellProfiler.main(["foo", "-b", "--html", "-o", path])
filenames = os.listdir(path)
self.assertTrue("index.html" in filenames)
finally:
shutil.rmtree(path)
def test_01_01_html(self):
path = tempfile.mkdtemp()
try:
CellProfiler.main(["foo", "-b", "--html","-o",path])
filenames = os.listdir(path)
self.assertTrue("index.html" in filenames)
finally:
shutil.rmtree(path)
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 = os.path.join(
example_images_directory(),
"ExampleHT29")
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")
args = [ "CellProfiler.py",
"-c", "-r", "-b",
"-i", input_directory,
"-o", output_directory,
"-p", pipeline_file,
"-d", done_file,
"-t", temp_directory,
measurements_file]
CellProfiler.main(args)
import cellprofiler.preferences as cpprefs
self.assertTrue(os.path.exists(measurements_file))
self.assertTrue(os.path.exists(done_file))
self.assertEqual(temp_directory, cpprefs.get_temporary_directory())
#
# Re-run using the measurements file.
#
m2_file = os.path.join(output_directory, "M2.h5")
args = [ "CellProfiler.py",
"-c", "-r", "-b",
"-i", input_directory,
"-o", output_directory,
"-p", measurements_file,
m2_file]
CellProfiler.main(args)
self.assertTrue(os.path.exists(m2_file))
finally:
shutil.rmtree(output_directory)
def test_01_02_code_statistics(self):
old_stdout = sys.stdout
fake_stdout = StringIO()
sys.stdout = fake_stdout
try:
CellProfiler.main(["foo", "-b", "--code-statistics"])
finally:
sys.stdout = old_stdout
fake_stdout.seek(0)
found_module_stats = False
found_setting_stats = False
found_lines_of_code = False
for line in fake_stdout.readlines():
if line.startswith("# of built-in modules"):
found_module_stats = True
elif line.startswith("# of settings"):
found_setting_stats = True
elif line.startswith("# of lines of code"):
found_lines_of_code = True
self.assertTrue(found_module_stats)
self.assertTrue(found_setting_stats)
self.assertTrue(found_lines_of_code)
def test_01_02_code_statistics(self):
old_stdout = sys.stdout
fake_stdout = StringIO()
sys.stdout = fake_stdout
try:
CellProfiler.main(["foo", "-b", "--code-statistics"])
finally:
sys.stdout = old_stdout
fake_stdout.seek(0)
found_module_stats = False
found_setting_stats = False
found_lines_of_code = False
for line in fake_stdout.readlines():
if line.startswith("# of built-in modules"):
found_module_stats = True
elif line.startswith("# of settings"):
found_setting_stats = True
elif line.startswith("# of lines of code"):
found_lines_of_code = True
self.assertTrue(found_module_stats)
self.assertTrue(found_setting_stats)
self.assertTrue(found_lines_of_code)
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 = os.path.join(example_images_directory(),
"ExampleHT29")
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")
args = [
"CellProfiler.py", "-c", "-r", "-b", "-i", input_directory,
"-o", output_directory, "-p", pipeline_file, "-d", done_file,
"-t", temp_directory, measurements_file
]
CellProfiler.main(args)
import cellprofiler.preferences as cpprefs
self.assertTrue(os.path.exists(measurements_file))
self.assertTrue(os.path.exists(done_file))
self.assertEqual(temp_directory, cpprefs.get_temporary_directory())
#
# Re-run using the measurements file.
#
m2_file = os.path.join(output_directory, "M2.h5")
args = [
"CellProfiler.py", "-c", "-r", "-b", "-i", input_directory,
"-o", output_directory, "-p", measurements_file, m2_file
]
CellProfiler.main(args)
self.assertTrue(os.path.exists(m2_file))
finally:
shutil.rmtree(output_directory)
