bcf-scape 0.1.0__py3-none-any.whl

bcf_scape-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: bcf-scape
+Version: 0.1.0
+Summary: SCAPE light-sheet microscopy data processing (deskewing, max-projection, batch I/O).
+Author: Tomas Skripcak
+Author-email: HongKee Moon <moon@mpi-cbg.de>
+Maintainer-email: "Scientific Computing Facility, MPI-CBG" <scicomp@mpi-cbg.de>
+License-Expression: BSD-3-Clause
+Project-URL: Homepage, https://git.mpi-cbg.de/scicomp/scidev_team/bcf_scape
+Project-URL: Source, https://git.mpi-cbg.de/scicomp/scidev_team/bcf_scape
+Project-URL: Issues, https://git.mpi-cbg.de/scicomp/scidev_team/bcf_scape/-/issues
+Keywords: scape,light-sheet,microscopy,deskew,ome-tiff,pyclesperanto
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: tifffile
+Requires-Dist: pyclesperanto
+Requires-Dist: pyclesperanto-prototype
+Requires-Dist: tomli_w
+Requires-Dist: tomli; python_version < "3.11"
+Requires-Dist: tqdm
+Requires-Dist: matplotlib
+Requires-Dist: ipywidgets
+Requires-Dist: Pillow
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Dynamic: license-file
+
+# bcf-scape
+
+`bcf-scape` is a modular Python library for processing **SCAPE light-sheet
+microscopy** data: deskewing OME-TIFF stacks, computing Z / Y max-projections,
+and batch-processing multi-position / multi-timepoint acquisitions.
+
+GPU-accelerated via [`pyclesperanto`](https://github.com/clEsperanto/pyclesperanto).
+
+Developed and maintained by the Scientific Computing Facility at MPI-CBG.
+
+## Installation
+
+```bash
+pip install bcf-scape
+```
+
+The package imports as `scape`:
+
+```python
+import scape
+```
+
+## Quick start
+
+### Command line
+
+```bash
+python -m scape.pipeline \
+    --settings settings.toml \
+    --tiff     /data/raw/scan.ome.tif \
+    --output   /data/processed/Deskewed/
+```
+
+or via the console script:
+
+```bash
+scape --help
+```
+
+### Python API
+
+```python
+from scape.config.settings import load_settings_from_file
+from scape.pipeline import run
+
+settings = load_settings_from_file("settings.toml")
+run(settings, "/data/raw/scan.ome.tif", "/data/processed/Deskewed/")
+```
+
+## TOML configuration
+
+`ProcessingSettings` round-trips to a human-readable TOML file:
+
+```python
+from scape.config.settings import ProcessingSettings
+
+settings = ProcessingSettings()
+settings.lightsheet_angle_in_degrees = 39
+settings.save_toml("my_run.toml")
+
+# Later …
+settings = ProcessingSettings.load_toml("my_run.toml")
+```
+
+## Modules
+
+| Module | Responsibility |
+| --- | --- |
+| `scape.pipeline` | End-to-end deskewing pipeline (CLI entry point) |
+| `scape.config.settings` | `ProcessingSettings` + TOML I/O |
+| `scape.metadata.parser` | OME-TIFF metadata extraction |
+| `scape.preprocessing.image_handler` | Channel/timepoint selection, dual-camera flips |
+| `scape.processing.deskew_engine` | Deskewing primitives |
+| `scape.batch.processor` | Multi-position / multi-timepoint orchestration |
+| `scape.output.saver` | TIFF writing helpers |
+| `scape.visualization.viewer` | Interactive Jupyter previews |
+
+## Citation
+
+If this package contributes to a publication, please acknowledge the
+Scientific Computing Facility at MPI-CBG. Contact `scicomp@mpi-cbg.de`
+for the formal citation entry.
+
+## Links
+
+* Source: <https://git.mpi-cbg.de/scicomp/scidev_team/bcf_scape>
+
+## License
+
+BSD-3-Clause. See [LICENSE](LICENSE).
+
+Copyright © 2026 Max Planck Institute of Molecular Cell Biology and Genetics
+(MPI-CBG).

bcf_scape-0.1.0.dist-info/RECORD

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bcf_scape-0.1.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: setuptools (82.0.1)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

bcf_scape-0.1.0.dist-info/entry_points.txt

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+[console_scripts]
+scape = scape.cli:main

bcf_scape-0.1.0.dist-info/licenses/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2026, Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

bcf_scape-0.1.0.dist-info/top_level.txt

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+scape

scape/__init__.py

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+"""
+SCAPE - Light Sheet Microscopy Image Processing Pipeline
+========================================================
+
+A modular Python library for processing light sheet microscopy data
+(deskewing, max-projection, batch processing of OME-TIFF stacks).
+
+Quick start
+-----------
+
+Run the pipeline from the command line::
+
+    python -m scape.pipeline \\
+        --settings settings.toml \\
+        --tiff     /data/raw/scan.ome.tif \\
+        --output   /data/processed/Deskewed/
+
+Or use the Python API::
+
+    from scape.config.settings import load_settings_from_file
+    from scape.pipeline import run
+
+    settings = load_settings_from_file("settings.toml")
+    run(settings, "/data/raw/scan.ome.tif", "/data/processed/Deskewed/")
+
+Main modules
+------------
+
+* :mod:`scape.pipeline`              – end-to-end processing entry point
+* :mod:`scape.config.settings`       – ``ProcessingSettings`` and TOML I/O
+* :mod:`scape.metadata.parser`       – OME-TIFF metadata extraction
+* :mod:`scape.preprocessing.image_handler` – channel/timepoint selection, flips
+* :mod:`scape.processing.deskew_engine`    – deskewing primitives
+* :mod:`scape.batch.processor`       – multi-position / multi-timepoint loops
+* :mod:`scape.output.saver`          – TIFF writing helpers
+* :mod:`scape.visualization.viewer`  – interactive Jupyter previews
+"""

scape/__main__.py

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+"""Allows ``python -m scape`` to invoke the CLI."""
+from scape.cli import main
+
+main()

scape/batch/__init__.py

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+"""
+Batch processing workflows for light sheet microscopy data.
+"""

scape/batch/processor.py

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+"""
+Batch processing workflow for light sheet microscopy data.
+"""
+
+import os
+import numpy as np
+from tqdm import tqdm
+
+
+class BatchProcessor:
+    """Manage batch processing workflows for light sheet microscopy data."""
+
+    def __init__(self, settings):
+        """
+        Initialize batch processor.
+
+        Args:
+            settings: ProcessingSettings object
+        """
+        self.settings = settings
+
+    def process_multiple_positions(self, tiff_file, output_folder, progress_bar=None):
+        """
+        Process multiple positions from a TIFF file.
+
+        Args:
+            tiff_file: TiffFile object
+            output_folder: Output folder path
+            progress_bar: Optional progress bar
+
+        Returns:
+            List of processed files
+        """
+        processed_files = []
+
+        # Determine positions to process
+        if self.settings.selected_positions == 0:
+            pos_list = list(range(len(tiff_file.series)))
+        else:
+            pos_list = self.settings.posList
+
+        # Process each position
+        for pp in pos_list:
+            img_array = tiff_file.series[pp]
+            image_xd = img_array.asarray()
+
+            # Process each channel
+            for jj in range(self.settings.number_channels):
+                if (
+                    self.settings.selected_channels == 1
+                    and jj not in self.settings.channelsList
+                ):
+                    if progress_bar:
+                        progress_bar.update(self.settings.number_timepoints)
+                    continue
+
+                # Process each timepoint
+                for kk in range(
+                    self.settings.timepoints_start,
+                    min(
+                        self.settings.timepoints_start + self.settings.timepoints_range,
+                        self.settings.number_timepoints,
+                    ),
+                ):
+                    # This would call the actual processing logic
+                    # Placeholder implementation
+                    if progress_bar:
+                        progress_bar.update(1)
+
+                    processed_files.append(
+                        f"Processed position {pp}, channel {jj}, timepoint {kk}"
+                    )
+
+        return processed_files
+
+    def process_separate_timepoints(
+        self, source_folder, output_folder, progress_bar=None
+    ):
+        """
+        Process files with separate timepoints.
+
+        Args:
+            source_folder: Source folder path
+            output_folder: Output folder path
+            progress_bar: Optional progress bar
+
+        Returns:
+            List of processed files
+        """
+        processed_files = []
+
+        # This would iterate through timepoint directories
+        # Placeholder implementation
+        for root, dirs, files in os.walk(source_folder):
+            for file in files:
+                if file.endswith(".tif"):
+                    # Process file
+                    if progress_bar:
+                        progress_bar.update(1)
+                    processed_files.append(file)
+
+        return processed_files
+
+    def setup_output_directories(self, output_folder):
+        """Create the standard output folder layout used by the pipeline.
+
+        Ensures ``output_folder`` exists and creates the ``MaxProject_Z`` and
+        ``MaxProject_Y`` sub-folders used by :class:`OutputSaver`. Idempotent;
+        existing folders are left alone.
+
+        Args:
+            output_folder: Root directory for the run. Created with
+                ``os.makedirs`` if missing.
+        """
+        directories = [
+            output_folder,
+            os.path.join(output_folder, "MaxProject_Z"),
+            os.path.join(output_folder, "MaxProject_Y"),
+        ]
+
+        for directory in directories:
+            if not os.path.exists(directory):
+                os.makedirs(directory)
+
+    def create_progress_bar(self, total_steps):
+        """
+        Create a progress bar for processing.
+
+        Args:
+            total_steps: Total number of steps
+
+        Returns:
+            Progress bar object
+        """
+        return tqdm(total=total_steps, desc="Processing files")