Example file didn't work well

When I tried to run the example, it reported the following errors.

2022-09-07 21:04:53,032:INFO:91:root: Execution arguments and environment saved to "/tmp/cytokit-example/cellular-marker/20181116-d40-r1-20x-5by5/output/v00/processor/execution/202209072104.json" 2022-09-07 21:05:00,776:INFO:91:cytokit.exec.pipeline: Starting Pre-processing pipeline for 1 tasks (1 workers) 2022-09-07 21:05:00,794:INFO:107:cytokit.data: Downloading url "https://storage.googleapis.com/microscope-image-quality/static/model/model.ckpt-1000042.index" to local path "/lab/data/.cytokit/cache/best_focus/model/model.ckpt-1000042.index" 2022-09-07 21:05:02,492:INFO:107:cytokit.exec.pipeline: Loaded tile 1 for region 1 [shape = (1, 7, 4, 1440, 1920)] 2022-09-07 21:05:05,007:INFO:107:cytokit.data: Downloading url "https://storage.googleapis.com/microscope-image-quality/static/model/model.ckpt-1000042.meta" to local path "/lab/data/.cytokit/cache/best_focus/model/model.ckpt-1000042.meta" 2022-09-07 21:05:06,764:INFO:107:cytokit.data: Downloading url "https://storage.googleapis.com/microscope-image-quality/static/model/model.ckpt-1000042.data-00000-of-00001" to local path "/lab/data/.cytokit/cache/best_focus/model/model.ckpt-1000042.data-00000-of-00001" Using TensorFlow backend. distributed.worker - WARNING - Compute Failed Function: run_preprocess_task args: ({'tile_prefetch_capacity': 1, 'op_flags': <cytokit.exec.pipeline.OpFlags object at 0x7f334cab47b8>, 'output_dir': '/tmp/cytokit-example/cellular-marker/20181116-d40-r1-20x-5by5/output/v00', 'gpu': 0, 'tile_indexes': array([0]), 'region_indexes': array([0]), 'data_dir': '/tmp/cytokit-example/cellular-marker/20181116-d40-r1-20x-5by5/raw'}) kwargs: {} Exception: OSError('Unable to open file (file signature not found)',)

Traceback (most recent call last): File "/usr/local/bin/cytokit", line 32, in main() File "/usr/local/bin/cytokit", line 28, in main fire.Fire(Cytokit) File "/opt/conda/envs/cytokit/lib/python3.5/site-packages/fire/core.py", line 127, in Fire component_trace = _Fire(component, args, context, name) File "/opt/conda/envs/cytokit/lib/python3.5/site-packages/fire/core.py", line 366, in _Fire component, remaining_args) File "/opt/conda/envs/cytokit/lib/python3.5/site-packages/fire/core.py", line 542, in _CallCallable result = fn(varargs, kwargs) File "/lab/repos/cytokit/python/pipeline/cytokit/cli/init.py", line 167, in run_all fn({config[op], params}) File "/lab/repos/cytokit/python/pipeline/cytokit/cli/processor.py", line 131, in run pipeline.run(pl_config, logging_init_fn=self._logging_init_fn) File "/lab/repos/cytokit/python/pipeline/cytokit/exec/pipeline.py", line 458, in run run_tasks(pl_conf, 'Pre-processing', run_preprocess_task, logging_init_fn) File "/lab/repos/cytokit/python/pipeline/cytokit/exec/pipeline.py", line 421, in run_tasks res = [r.result() for r in res] File "/lab/repos/cytokit/python/pipeline/cytokit/exec/pipeline.py", line 421, in res = [r.result() for r in res] File "/opt/conda/envs/cytokit/lib/python3.5/site-packages/distributed/client.py", line 227, in result six.reraise(result) File "/opt/conda/envs/cytokit/lib/python3.5/site-packages/six.py", line 702, in reraise raise value.with_traceback(tb) File "/lab/repos/cytokit/python/pipeline/cytokit/exec/pipeline.py", line 441, in run_preprocess_task return run_task(task, ops, preprocess_tile) File "/lab/repos/cytokit/python/pipeline/cytokit/exec/pipeline.py", line 355, in run_task with ops: File "/lab/repos/cytokit/python/pipeline/cytokit/ops/op.py", line 200, in enter v.enter() File "/lab/repos/cytokit/python/pipeline/cytokit/ops/op.py", line 152, in enter self.initialize() File "/lab/repos/cytokit/python/pipeline/cytokit/ops/cytometry.py", line 136, in initialize self.cytometer.initialize() File "/lab/repos/cytokit/python/pipeline/cytokit/cytometry/cytometer.py", line 610, in initialize self.model.load_weights(self.weights_path or self._get_weights_path()) File "/opt/conda/envs/cytokit/lib/python3.5/site-packages/keras/engine/network.py", line 1157, in load_weights with h5py.File(filepath, mode='r') as f: File "/opt/conda/envs/cytokit/lib/python3.5/site-packages/h5py/_hl/files.py", line 408, in init swmr=swmr) File "/opt/conda/envs/cytokit/lib/python3.5/site-packages/h5py/_hl/files.py", line 173, in make_fid fid = h5f.open(name, flags, fapl=fapl) File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py/h5f.pyx", line 88, in h5py.h5f.open OSError: Unable to open file (file signature not found) Traceback (most recent call last): File "/usr/local/bin/cytokit", line 32, in main() File "/usr/local/bin/cytokit", line 28, in main fire.Fire(Cytokit) File "/opt/conda/envs/cytokit/lib/python3.5/site-packages/fire/core.py", line 127, in Fire component_trace = _Fire(component, args, context, name) File "/opt/conda/envs/cytokit/lib/python3.5/site-packages/fire/core.py", line 366, in _Fire component, remaining_args) File "/opt/conda/envs/cytokit/lib/python3.5/site-packages/fire/core.py", line 542, in _CallCallable result = fn(varargs, kwargs) File "/lab/repos/cytokit/python/pipeline/cytokit/cli/init.py", line 167, in run_all fn({config[op], params}) File "/lab/repos/cytokit/python/pipeline/cytokit/cli/operator.py", line 135, in extract z_slice_fn = _get_z_slice_fn(z, self.data_dir) File "/lab/repos/cytokit/python/pipeline/cytokit/cli/operator.py", line 78, in _get_z_slice_fn map = function_data.get_best_focus_coord_map(data_dir) File "/lab/repos/cytokit/python/pipeline/cytokit/function/data.py", line 45, in get_best_focus_coord_map return get_best_focus_data(output_dir).set_index(['region_index', 'tile_x', 'tile_y'])['best_z'].to_dict() File "/lab/repos/cytokit/python/pipeline/cytokit/function/data.py", line 31, in get_best_focus_data processor_data, path = get_processor_data(output_dir, return_path=True) File "/lab/repos/cytokit/python/pipeline/cytokit/function/data.py", line 19, in get_processor_data proc_data = exec.read_processor_data(path) File "/lab/repos/cytokit/python/pipeline/cytokit/exec/init.py", line 34, in read_processor_data with open(path, 'r') as fd: FileNotFoundError: [Errno 2] No such file or directory: '/tmp/cytokit-example/cellular-marker/20181116-d40-r1-20x-5by5/output/v00/processor/data.json' 2022-09-07 21:07:19,050:INFO:189:root: Running cytometry statistics aggregation 2022-09-07 21:07:19,051:WARNING:189:cytokit.cytometry.data: Expected cytometry data file at "/tmp/cytokit-example/cellular-marker/20181116-d40-r1-20x-5by5/output/v00/cytometry/statistics/R001_X001_Y001.csv" does not exist. It will be ignored but this may be worth investigating Traceback (most recent call last): File "/usr/local/bin/cytokit", line 32, in main() File "/usr/local/bin/cytokit", line 28, in main fire.Fire(Cytokit) File "/opt/conda/envs/cytokit/lib/python3.5/site-packages/fire/core.py", line 127, in Fire component_trace = _Fire(component, args, context, name) File "/opt/conda/envs/cytokit/lib/python3.5/site-packages/fire/core.py", line 366, in _Fire component, remaining_args) File "/opt/conda/envs/cytokit/lib/python3.5/site-packages/fire/core.py", line 542, in _CallCallable result = fn(varargs, kwargs) File "/lab/repos/cytokit/python/pipeline/cytokit/cli/init.py", line 167, in run_all fn({config[op], params}) File "/lab/repos/cytokit/python/pipeline/cytokit/cli/analysis.py", line 28, in aggregate_cytometry_statistics self.data_dir, self.config, mode=mode, export_csv=export_csv, export_fcs=export_fcs, variant=variant) File "/lab/repos/cytokit/python/pipeline/cytokit/function/core.py", line 19, in aggregate_cytometry_statistics res = function_data.get_cytometry_data(output_dir, config, mode=mode) File "/lab/repos/cytokit/python/pipeline/cytokit/function/data.py", line 59, in get_cytometry_data cyto_data = cytometry_data.aggregate(config, output_dir) File "/lab/repos/cytokit/python/pipeline/cytokit/cytometry/data.py", line 32, in aggregate df = pd.concat(df) File "/opt/conda/envs/cytokit/lib/python3.5/site-packages/pandas/core/reshape/concat.py", line 212, in concat copy=copy) File "/opt/conda/envs/cytokit/lib/python3.5/site-packages/pandas/core/reshape/concat.py", line 245, in init raise ValueError('No objects to concatenate') ValueError: No objects to concatenate

Do you have any ideas to figure out the issue? Thanks a lot.

hammerlab / cytokit

Example file didn't work well #43