# Module Documentation

(autogenerated by `util_doc.py`)

- [asyncio_tools](apidocs/chimcla/chimcla.asyncio_tools.md)
    - Lines: 52
    - Docstring:
        >
        >
        > Helper module; provides useful functions for running python code in background or in parallel.
        >
        >
- [aux_rename_cell_imgs](apidocs/chimcla/chimcla.aux_rename_cell_imgs.md)
    - Lines: 44
    - Docstring:
        >
        >
        > This script renames image files, such that the cell comes first.
        >
        >
- [cli](apidocs/chimcla/chimcla.cli.md)
    - Lines: 244
    - Docstring:
        >
        >
        > **Important**
        >
        > Command line interface.
        >
        >
- [log_time_filter](apidocs/chimcla/chimcla.log_time_filter.md)
    - Lines: 97
    - Docstring:
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        >
        > This script is used to filter log file by timestamps
        >
        >
        >
- [release](apidocs/chimcla/chimcla.release.md)
    - Lines: 4
    - Docstring:
        >
        >
        > Define the version number of chimcla. Nothing else.
        >
        >
- [stage_0f_resize_and_jpg](apidocs/chimcla/chimcla.stage_0f_resize_and_jpg.md)
    - Lines: 88
    - Docstring:
        >
        >
        >
        > This module is probably obsolete
        > (and not included in the chimcla command line interface (see `cli.py`))
        >
        > - Convert images to jpg (originally we used .png) and resize width to 1000px.
        > - uses `asyncio` to allow for parallel processing → speedup
        > - "0f" comes from some internal versioning which enumerated the necessary processing steps
        >
        >
- [stage_1a_preprocessing](apidocs/chimcla/chimcla.stage_1a_preprocessing.md)
    - Lines: 319
    - Docstring:
        >
        >
        > This module contains several preprocessing steps which were distributed over
        > multiple scripts in earlier versions.
        >
        > Contains class `Stage1Preprocessor` with method pipeline(self, fpath):
        >
        > - self.step01_mogrify_1000jpg(iic)
        > - self.step02_empty_slot_detection(iic)
        > - self.step03_cropping(iic)
        > - self.step04_shading_correction(iic)
        >
        >
        >
- [stage_2a1_bar_selection_new](apidocs/chimcla/chimcla.stage_2a1_bar_selection_new.md)
    - Lines: 722
    - Docstring:
        >
        >
        > This Module is a (yet incomplete) rewrite of the historically grown module stage_2a_bar_selection.
        > It should eventually replace it. Currently it is only used in the tests.
        >
        >
- [stage_2a_bar_selection](apidocs/chimcla/chimcla.stage_2a_bar_selection.md)
    - Lines: 2749
    - Docstring:
        >
        >
        > **Important**
        >
        > Historically grown and messy module for bar selection (or "separation")
        >
        > - contains:
        >     - class `CavityCarrierImageAnalyzer` ("FormenTrägerBildAnalyzer")
        >     - class `ExtendedSqliteDict`
        >
        >
- [stage_2b_bar_C0_hist_dict](apidocs/chimcla/chimcla.stage_2b_bar_C0_hist_dict.md)
    - Lines: 146
    - Docstring:
        >
        >
        > Command line interface script for functionality from stage_2a_bar_selection.
        >
        > Main feature: run the time-consuming tasks in parallel (using asyncio_tools)
        >
        > Not yet included in chimcla.cli
        >
        > Maybe obsolete?
        >
        >
- [stage_2c_hist_based_anomaly_detection](apidocs/chimcla/chimcla.stage_2c_hist_based_anomaly_detection.md)
    - Lines: 23
    - Docstring:
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        >
        > Very short wrapper for `HistEvaluation.find_critical_cells()`
        >
        >
- [stage_3a_hist_based_classification](apidocs/chimcla/chimcla.stage_3a_hist_based_classification.md)
    - Lines: 191
    - Docstring:
        >
        >
        > This script creates histogram style plots for every unusual cell
        > (without considering the area (=number of affected pixels))
        >
        > - uses `asyncio_tools` to spawn multiple workers
        > - not so important (maybe obsolete?)
        >
        >
- [stage_3b_hist_area_based_classification](apidocs/chimcla/chimcla.stage_3b_hist_area_based_classification.md)
    - Lines: 207
    - Docstring:
        >
        >
        > This script creates histogram style plots for every unusual cell (also considering the area)
        >
        > - uses asyncio_tools to spawn multiple workers
        > - Not yet included in chimcla.cli.py
        >
        >
- [stage_3c_create_file_names](apidocs/chimcla/chimcla.stage_3c_create_file_names.md)
    - Lines: 248
    - Docstring:
        >
        >
        > This program creates copies or symlinks of files to enable simple sorting wrt.
        > one numeric feature (s-value).
        >
        > Also contains `create_json_data(...)`
        >
        > - Not yet included in `chimcla.cli`.
        >
        >
        >
- [stage_3d_create_experimental_data](apidocs/chimcla/chimcla.stage_3d_create_experimental_data.md)
    - Lines: 488
    - Docstring:
        >
        >
        > This file serves for
        > - creating images for Romys Chocolate Experiment (as discussed in Nov. 2023)
        > - creating data (images and numerical) for history evaluation
        >
        >
        >
- [stage_3e_create_experimental_data_csv](apidocs/chimcla/chimcla.stage_3e_create_experimental_data_csv.md)
    - Lines: 227
    - Docstring:
        >
        >
        > Script to generate csv data files for Romys Chocolate experiments (late 2024/early 2024)"
        >
        >
- [util](apidocs/chimcla/chimcla.util.md)
    - Lines: 112
    - Docstring:
        >
        >
        > Important:
        >
        > This module contains general utility functions used in other chimcla modules.
        >
        > - ImageInfoContainer
        >
        > **TODO**: code from other (util) modules might be ported to here to improve code architecture
        >
        >
- [util_doc](apidocs/chimcla/chimcla.util_doc.md)
    - Lines: 118
    - Docstring:
        >
        >
        > Module to prepare and execute the generation of documentation (via sphinx).
        >
        > used by some `chimcla ...` commands.
        >
        >
- [util_file_sorting](apidocs/chimcla/chimcla.util_file_sorting.md)
    - Lines: 164
    - Docstring:
        >
        >
        > This Module contains classes and functions for the *Lot Preparation*
        > step of the processing pipeline.
        >
        > used by cli.py.
        >
        >
- [util_img](apidocs/chimcla/chimcla.util_img.md)
    - Lines: 29
    - Docstring:
        >
        >
        > Contains two image short related utility functions.
        >
        > Currently only used in stage_2a1_bar_selection_new.py.
        >
        > TODO: merge into util.py?
        >
        >
- [util_sort_into_folder](apidocs/chimcla/chimcla.util_sort_into_folder.md)
    - Lines: 59
    - Docstring:
        >
        >
        > Helper script to copy images into different class directories based on
        > a hardcoded csv file (e.g. containing the result of manual labeling).
        >
        > Not yet included in cli.py.
        >
        >
- [util_step_history_from_logfile](apidocs/chimcla/chimcla.util_step_history_from_logfile.md)
    - Lines: 712
    - Docstring:
        >
        >
        > This script is used to evaluate the logfile to create the step history images.
        >
        > example call:
        > python step_history_from_logfile.py -l ~/mnt/XAI-DIA-gl/Carsten/logs/classifier-2023-07-10_since_2023-06-26.log
        >
        > Not yet included in cli.py.
        >
        >
        >