Viewing Clear Control

Example of opening a Clear Control dataset and viewing with napari.

Usage:

$ python view_clearcontrol_dataset.py <OPTIONAL Clear Control dataset>

If the dataset path is not provided, it creates a mock dataset of random integers.

Setup

import sys
import tempfile
import time

from iohub.clearcontrol import (
    ClearControlFOV,
    create_mock_clear_control_dataset,
)

Parse optional Clear Control dataset path. Mock dataset is created if dataset path is not provided.

if len(sys.argv) < 2:
    print("Loading mock random noise dataset ...")
    path = f"{tempfile.gettempdir()}/dataset.cc"
    create_mock_clear_control_dataset(path)
else:
    path = sys.argv[1]

Loading mock random noise dataset ...

Open Clear Control dataset.

s = time.time()
cc = ClearControlFOV(path, cache=True)
print("init time (secs)", time.time() - s)

init time (secs) 0.0001285076141357422

Time load time of a single volume.

s = time.time()
cc[0, 0]
print("single volume load time (secs)", time.time() - s)

Traceback (most recent call last):
  File "/tmp/tmp6ck5egm1/docs/examples/run_view_clearcontrol_dataset.py", line 49, in <module>
    cc[0, 0]
    ~~^^^^^^
  File "/tmp/tmp6ck5egm1/iohub/clearcontrol.py", line 325, in __getitem__
    return self._load_array(key)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp6ck5egm1/iohub/clearcontrol.py", line 125, in _key_cache_wrapper
    self._cache_array = f(self, key)
                        ^^^^^^^^^^^^
  File "/tmp/tmp6ck5egm1/iohub/clearcontrol.py", line 335, in _load_array
    shape = self.shape
            ^^^^^^^^^^
  File "/tmp/tmp6ck5egm1/iohub/clearcontrol.py", line 192, in shape
    last_line = f.readlines()[-1].decode("utf-8")
                ~~~~~~~~~~~~~^^^^
IndexError: list index out of range

Load dataset using napari

if __name__ == "__main__":
    try:
        import napari

        s = time.time()
        napari.view_image(cc)
        print("napari load time (secs)", time.time() - s)

        napari.run()

    except ModuleNotFoundError:
        pass