def start_workflow_create_project_headless(self, workflow_class_tuple,
temp_dir):
"""Tests project file creation via the command line
Args:
workflow_class_tuple (tuple): tuple returned from getAvailableWorkflows
with (workflow_class, workflow_name, workflow_class.workflowDisplayName)
"""
workflow_class, workflow_name, display_name = workflow_class_tuple
logger.debug(f"starting {workflow_name}")
project_file = generate_project_file_name(temp_dir, workflow_name)
args = [
"--headless", f"--new_project={project_file}",
f"--workflow={workflow_name}"
]
# Clear the existing commandline args so it looks like we're starting fresh.
sys.argv = ["ilastik.py"]
sys.argv.extend(args)
# Start up the ilastik.py entry script as if we had launched it from the command line
parsed_args, workflow_cmdline_args = ilastik_main.parse_known_args()
shell = ilastik_main.main(parsed_args=parsed_args,
workflow_cmdline_args=workflow_cmdline_args,
init_logging=False)
shell.closeCurrentProject()
# now check if the project file has been created:
assert os.path.exists(
project_file
), f"Project File {project_file} creation not successful"
def start_workflow_load_project_headless(self, workflow_class_tuple, temp_dir):
"""Tests opening project files in headless mode via the command line
Args:
workflow_class_tuple (tuple): tuple returned from getAvailableWorkflows
with (workflow_class, workflow_name, workflow_class.workflowDisplayName)
"""
workflow_class, workflow_name, display_name = workflow_class_tuple
logger.debug(f'starting {workflow_name}')
project_file = generate_project_file_name(temp_dir, workflow_name)
self.create_project_file(workflow_class, project_file)
assert os.path.exists(project_file), f"Project File {project_file} creation not successful"
args = [
'--headless',
f'--project={project_file}',
]
# Clear the existing commandline args so it looks like we're starting fresh.
sys.argv = ['ilastik.py']
sys.argv.extend(args)
# Start up the ilastik.py entry script as if we had launched it from the command line
parsed_args, workflow_cmdline_args = ilastik_main.parse_known_args()
shell = ilastik_main.main(
parsed_args=parsed_args, workflow_cmdline_args=workflow_cmdline_args, init_logging=False)
shell.closeCurrentProject()
def create_test_files():
tags = vigra.defaultAxistags("zyxc")
tags['x'].resolution = 1.0
tags['y'].resolution = 1.0
tags['z'].resolution = 45.0
tags['c'].description = 'intensity'
with h5py.File(test_data_path, 'w') as f:
f['zeros'] = numpy.zeros( (10, 100, 200, 1), dtype=numpy.uint8 )
f['zeros'].attrs['axistags'] = tags.toJSON()
import ilastik_main
parsed_args, workflow_cmdline_args = ilastik_main.parse_known_args()
parsed_args.new_project = test_project_path
parsed_args.workflow = "Pixel Classification"
parsed_args.headless = True
shell = ilastik_main.main(parsed_args, workflow_cmdline_args)
data_selection_applet = shell.workflow.dataSelectionApplet
# To configure data selection, start with empty cmdline args and manually fill them in
data_selection_args, _ = data_selection_applet.parse_known_cmdline_args([])
data_selection_args.raw_data = [test_data_path + '/zeros']
# Configure
data_selection_applet.configure_operator_with_parsed_args(data_selection_args)
shell.projectManager.saveProject()
return data_selection_applet
def create_test_files():
tags = vigra.defaultAxistags("zyxc")
tags['x'].resolution = 1.0
tags['y'].resolution = 1.0
tags['z'].resolution = 45.0
tags['c'].description = 'intensity'
with h5py.File(test_data_path, 'w') as f:
f['zeros'] = numpy.zeros((10, 100, 200, 1), dtype=numpy.uint8)
f['zeros'].attrs['axistags'] = tags.toJSON()
import ilastik_main
parsed_args, workflow_cmdline_args = ilastik_main.parse_known_args()
parsed_args.new_project = test_project_path
parsed_args.workflow = "Pixel Classification"
parsed_args.headless = True
shell = ilastik_main.main(parsed_args, workflow_cmdline_args)
data_selection_applet = shell.workflow.dataSelectionApplet
# To configure data selection, start with empty cmdline args and manually fill them in
data_selection_args, _ = data_selection_applet.parse_known_cmdline_args(
[])
data_selection_args.raw_data = [test_data_path + '/zeros']
# Configure
data_selection_applet.configure_operator_with_parsed_args(
data_selection_args)
shell.projectManager.saveProject()
return data_selection_applet
def open_test_files():
import ilastik_main
parsed_args, workflow_cmdline_args = ilastik_main.parse_known_args()
parsed_args.project = test_project_path
parsed_args.headless = True
shell = ilastik_main.main(parsed_args, workflow_cmdline_args)
return shell.workflow.dataSelectionApplet
def open_test_files():
import ilastik_main
parsed_args, workflow_cmdline_args = ilastik_main.parse_known_args()
parsed_args.project = test_project_path
parsed_args.headless = True
shell = ilastik_main.main(parsed_args, workflow_cmdline_args)
return shell.workflow.dataSelectionApplet
def test_133_pc_oc_loading(project_path: pathlib.Path):
args = ["--headless", f"--project={project_path}"]
# Clear the existing commandline args so it looks like we're starting fresh.
sys.argv = ["ilastik.py"]
sys.argv.extend(args)
# Start up the ilastik.py entry script as if we had launched it from the command line
parsed_args, workflow_cmdline_args = ilastik_main.parse_known_args()
shell = ilastik_main.main(parsed_args=parsed_args,
workflow_cmdline_args=workflow_cmdline_args,
init_logging=False)
shell.closeCurrentProject()
def main():
if '--clean_paths' in sys.argv:
script_dir = pathlib.Path(__file__).parent
ilastik_root = script_dir.parent.parent
_clean_paths(ilastik_root)
# Allow to start-up by double-clicking a project file.
if len(sys.argv) == 2 and sys.argv[1].endswith('.ilp'):
sys.argv.insert(1, '--project')
arg_opts, env_vars = _parse_internal_config("internal-startup-options.cfg")
sys.argv[1:1] = arg_opts
os.environ.update(env_vars)
import ilastik_main
parsed_args, workflow_cmdline_args = ilastik_main.parse_known_args()
hShell = ilastik_main.main(parsed_args, workflow_cmdline_args)
# in headless mode the headless shell is returned and its project manager still has an open project file
hShell.closeCurrentProject()
def main():
if '--clean_paths' in sys.argv:
script_dir = pathlib.Path(__file__).parent
ilastik_root = script_dir.parent.parent
_clean_paths(ilastik_root)
# Allow to start-up by double-clicking a project file.
if len(sys.argv) == 2 and sys.argv[1].endswith('.ilp'):
sys.argv.insert(1, '--project')
arg_opts, env_vars = _parse_internal_config("internal-startup-options.cfg")
sys.argv[1:1] = arg_opts
os.environ.update(env_vars)
import ilastik_main
parsed_args, workflow_cmdline_args = ilastik_main.parse_known_args()
hShell = ilastik_main.main(parsed_args, workflow_cmdline_args)
# in headless mode the headless shell is returned and its project manager still has an open project file
hShell.closeCurrentProject()