refactor ic #20
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refactor ic #20
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jenna-tomkinson
approved these changes
Jan 8, 2025
| # In[1]: | ||
| # In[ ]: |
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Recommend double checking this.
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| # In[2]: | ||
| # In[ ]: |
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| # get the list of dirs in the raw_data_path | ||
| dirs = [x for x in preprocessed_data_path.iterdir() if x.is_dir()] | ||
| # get the list of all dirs in the dir | ||
| for dir in dirs: | ||
| # get the list of all dirs in the dir | ||
| subdirs = [x for x in dir.iterdir() if x.is_dir()] | ||
| for subdir in subdirs: | ||
| run_name = f"{dir.name}_{subdir.name}" | ||
| if "4ch" in dir.name: | ||
| dict_of_inputs[run_name] = { | ||
| "path_to_images": pathlib.Path(subdir).resolve(strict=True), | ||
| "path_to_output": pathlib.Path(illum_directory / run_name).resolve(), | ||
| "path_to_pipeline": pathlib.Path( | ||
| "../pipelines/illum_4ch.cppipe" | ||
| ).resolve(), | ||
| } | ||
| elif "2ch" in dir.name: | ||
| dict_of_inputs[run_name] = { | ||
| "path_to_images": pathlib.Path(subdir).resolve(strict=True), | ||
| "path_to_output": pathlib.Path(illum_directory / run_name).resolve(), | ||
| "path_to_pipeline": pathlib.Path( | ||
| "../pipelines/illum_2ch.cppipe" | ||
| ).resolve(), | ||
| } | ||
| else: | ||
| ValueError("The directory name does not contain 2ch or 4ch") |
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Love seeing this more automated!
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| # ## Run `illum.cppipe` pipeline and calculate + save IC images | ||
| # This last cell does not get run as we run this pipeline in the command line. |
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Recommend confirming if the IC images are saved or the npy function, just in case.
| # In[1]: | ||
| # In[ ]: |
| # There are two channels in the terminal dataset: | ||
| # Channel 1: DAPI | ||
| # Channel 5: Annexin V | ||
| # | ||
| # Note that Channel 5 does not exists in the main dataset (13 time points), only the terminal timepoints. | ||
| # Note that Channel 5 does not exists in the first 13 time points only the terminal timepoints. |
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Suggested change
| # Note that Channel 5 does not exists in the first 13 time points only the terminal timepoints. | |
| # Note that Channel 5 does not exist in the first 13 time points, only the terminal time points. |
| @@ -0,0 +1 @@ | |||
| {"data_config": {"n_workers": 1, "working_dir": ".", "database": "sqlite", "address": null}, "segmentation_config": {"min_area": 30, "max_area": 1250, "n_workers": 8, "min_frontier": 0.0, "threshold": 0.5, "max_noise": 0.0, "ws_hierarchy": "area", "anisotropy_penalization": 0.0}, "linking_config": {"max_distance": 45, "n_workers": 8, "max_neighbors": 5, "distance_weight": 0.0, "z_score_threshold": 5.0}, "tracking_config": {"solver_name": "CBC", "appear_weight": -1, "disappear_weight": -1, "division_weight": -0.1, "n_threads": -1, "window_size": null, "overlap_size": 1, "solution_gap": 0.0, "time_limit": 36000, "method": 0, "link_function": "power", "power": 4, "bias": -0.001, "dismiss_weight_guess": null, "include_weight_guess": null}} | |||
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Looks like there is a no new endline error here.
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This PR refactors the IC module to be more parallelized across well-FOV