fibermorph-v2 by ezhil384 · Pull Request #16 · lasisilab/fibermorph

ezhil384 · 2026-07-03T19:50:55Z

New version of fibermorph

- README: remove HuggingFace Spaces YAML frontmatter (was rendering as raw text on GitHub) - packages.txt: replace libgl1-mesa-glx (removed in Debian bookworm/trixie) with libgl1 - requirements.txt: use -e ".[gui]" to include matplotlib and seaborn for the Streamlit Cloud visualizations tab - streamlit_app.py: replace main() call (removed in new app.py) with exec() pattern so Streamlit's re-run model works correctly - test.yaml: drop poetry in favour of plain pip (avoids poetry.lock sync issues after adding opencv-python-headless); add libgl1/libglib2.0-0 apt step; run tests on feature/** branches too - conventional-prs.yaml: mark title check continue-on-error in fork (advisory only; lasisilab enforces it on the upstream PR) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

…flict libglib2.0-0 from Bullseye repos requires libffi7 which is not available on the Trixie-based Streamlit Cloud image. opencv-python-headless needs no system GL libraries, so packages.txt can be empty. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

…as package names apt-get was trying to install each word of the comment as a package.

Streamlit Cloud now runs Python 3.14.4. The previous caret constraints (^1.26.4 for numpy, ^0.22 for scikit-image, ^10.2 for pillow) forced pip to use source distributions that fail to compile on Python 3.14. Widening to >=X allows pip to resolve pre-built wheels for newer minor versions. Also remove quotes around .[gui] in requirements.txt for uv compatibility.

app.py was calling segment_section() with sam2_checkpoint=/sam2_cfg= (hair_analysis names) but section_sam2.py defines checkpoint=/model_cfg=.

- TestComputeEFD: access efd["efd_coeffs"] instead of treating return value as ndarray directly - TestComputeRadialProfile: update key names to radial_* prefix, replace missing radius_range_mu with computed radial_max - radial_min, add n_radial_peaks to expected key set - TestExtractFeaturesFromArray: fix call signature (resolution_mu=, source_name=), adapt assertions for dict return type, fix efd key count (51 not 40), fix hu prefix (no underscore) - TestClassifyShape: add n_radial_peaks and asymmetry_index to all feature dicts (now required by classify_shape) - test_section_pipeline: fix hu column prefix from hu_ to hu - TestCurlIndex: make _curved_skel dense enough to avoid disconnected segments causing nan; fix assertion direction (chord/arc metric gives lower values for curved lines, not higher) Agent-Logs-Url: https://github.com/ezhil384/fibermorph/sessions/86945c40-fef0-4344-97fa-c44ac3c5e80d Co-authored-by: ezhil384 <80913303+ezhil384@users.noreply.github.com>

…ctored-version fix(tests): align test suite with refactored v2 API

Feature/v2 enhanced analysis

eraser-labs · 2026-07-03T19:51:54Z

fibermorph-architecture

View in eraser

Updated as of commit: d06b3eca317f09837f12408764774c56dba5a92c

Changed Files

Relevant Files

fibermorph/main.py
fibermorph/cli.py
fibermorph/fibermorph.py
fibermorph/workflows.py
fibermorph/analysis/section_pipeline.py
fibermorph/analysis/curvature_pipeline.py
fibermorph/analysis/parallel.py
fibermorph/io/readers.py
fibermorph/io/writers.py
fibermorph/io/converters.py
fibermorph/core/section.py
fibermorph/core/curvature.py
fibermorph/core/filters.py
fibermorph/core/shape_analysis.py
fibermorph/processing/section_sam2.py
fibermorph/pipeline/batch.py
fibermorph/gui/app.py
fibermorph/gui/visualizations.py
fibermorph/processing/binary.py
fibermorph/processing/morphology.py
fibermorph/processing/geometry.py
fibermorph/utils/filesystem.py
fibermorph/utils/metadata.py
fibermorph/utils/timing.py
fibermorph/fibermorph_compat.py
fibermorph/demo/dummy_data.py
fibermorph/gui/launcher.py

Diagram Syntax

title CI Pipeline Workflow

Developer [icon: user, color: blue]
GitHub [icon: github]
CI Runner [icon: server, color: green]
Cache Service [icon: database, color: orange]
Test Environment [icon: tool, color: green]
Artifact Storage [icon: archive, color: orange]

Developer > GitHub: Push code changes
activate Developer
GitHub > CI Runner: Trigger workflow

CI Runner > CI Runner: Set up environment
CI Runner > Cache Service: Check for cached dependencies

alt [label: cache exists, icon: check] {
  Cache Service > CI Runner: Return cached dependencies
}
else [label: cache miss, icon: x] {
  CI Runner > CI Runner: Install dependencies
  CI Runner > Cache Service: Store dependencies in cache
}

CI Runner > CI Runner: Install project dependencies

par [label: parallel jobs, icon: layers] {
  CI Runner > Test Environment: Run linting checks
}
and {
  CI Runner > Test Environment: Run unit tests
}
and {
  CI Runner > Test Environment: Run integration tests
}

loop [label: retry on failure, icon: refresh-cw] {
  Test Environment > Test Environment: Execute test suite
}

opt [label: tests pass, icon: check-circle] {
  CI Runner > Artifact Storage: Upload test results
  CI Runner > Artifact Storage: Upload coverage report
}

alt [label: all checks pass, icon: thumbs-up] {
  CI Runner > GitHub: Report success status
  GitHub > Developer: Notify build passed
}
else [label: checks fail, icon: thumbs-down] {
  CI Runner > GitHub: Report failure status
  GitHub > Developer: Notify build failed
}

deactivate Developer

Copilot

Pull request overview

This PR introduces the “fibermorph v2” release, expanding the analysis pipelines (extended section/curvature metrics), adding optional SAM2-based cross-section segmentation with CPU fallback, and updating deployment/testing assets (Streamlit + Docker + CI).

Changes:

Bump package to 2.0.0 and add/adjust dependencies + extras for GUI/viz and headless environments.
Add new functionality: batch pipeline, extended feature extraction, CLAHE curvature path, and optional SAM2 segmentation module.
Expand tests substantially and update deployment docs / Docker / GitHub Actions workflows.

Reviewed changes

Copilot reviewed 31 out of 77 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
tools/inventory_imports.py	Formatting-only update for the import inventory helper script.
test_py313.sh	Formatting-only update for the Python 3.13 install test script.
test_installation.sh	Formatting-only update for multi-version install test script.
STREAMLIT_DEPLOYMENT.md	Streamlit deployment doc expanded (now also documents Hugging Face Spaces Docker path).
streamlit_app.py	Switches Streamlit entrypoint to `exec`-based re-run behavior.
requirements.txt	Streamlit deployment requirements now install editable package with `[gui]` extras.
pyproject.toml	Bumps version to 2.0.0; updates dependency constraints; expands extras.
packages.txt	Removes Streamlit Cloud system package list.
LICENSE	Formatting-only (line-numbered diff) change.
fibermorph/utils/timing.py	Formatting-only (line-numbered diff) change.
fibermorph/utils/metadata.py	Adds filename metadata parsing and image collection utilities.
fibermorph/utils/logging_config.py	Formatting-only (line-numbered diff) change.
fibermorph/utils/filesystem.py	Formatting-only (line-numbered diff) change.
fibermorph/test/test_utils_timing.py	Formatting-only (line-numbered diff) change.
fibermorph/test/test_utils_metadata.py	Adds tests for `utils.metadata` (parse + directory scan).
fibermorph/test/test_utils_filesystem.py	Formatting-only (line-numbered diff) change.
fibermorph/test/test_section_pipeline.py	Adds tests for updated section pipeline behavior/extended features.
fibermorph/test/test_processing_binary.py	Formatting-only (line-numbered diff) change.
fibermorph/test/test_pipeline_batch.py	Adds tests for per-sample aggregation logic.
fibermorph/test/test_io_writers.py	Formatting-only (line-numbered diff) change.
fibermorph/test/test_io_readers.py	Formatting-only (line-numbered diff) change.
fibermorph/test/test_curvature_pipeline.py	Adds tests for CLAHE path + extended curvature outputs.
fibermorph/test/test_core_shape_analysis.py	Adds unit tests for new shape-analysis feature extraction/classification APIs.
fibermorph/test/test_core_filters.py	Extends filter tests; adds coverage for CLAHE filter path.
fibermorph/test/test_core_curvature_extended.py	Adds tests for new extended curvature metrics (curl index, wave count).
fibermorph/test_data/SimArcData/Oct06_1855_32_017780_arc_data.csv	Formatting-only (line-numbered diff) change.
fibermorph/test_data/SimArcData/Oct06_1855_32_017780_arc_data_errordata.csv	Formatting-only (line-numbered diff) change.
fibermorph/processing/section_sam2.py	New optional SAM2 segmentation module with watershed fallback.
fibermorph/processing/geometry.py	Formatting-only (line-numbered diff) change.
fibermorph/processing/binary.py	Formatting-only (line-numbered diff) change.
fibermorph/pipeline/batch.py	Adds batch runner + per-sample aggregation.
fibermorph/pipeline/init.py	Adds pipeline package init (file presence).
fibermorph/io/writers.py	Formatting-only (line-numbered diff) change.
fibermorph/io/readers.py	Formatting-only (line-numbered diff) change.
fibermorph/io/converters.py	Reorders optional `rawpy` import (still optional).
fibermorph/gui/launcher.py	Formatting-only (line-numbered diff) change.
fibermorph/gui/init.py	Formatting-only (line-numbered diff) change.
fibermorph/fibermorph.py	Formatting-only (line-numbered diff) change.
fibermorph/fibermorph_compat.py	Formatting-only (line-numbered diff) change.
fibermorph/demo/init.py	Formatting-only (line-numbered diff) change.
fibermorph/core/filters.py	Adds `filter_curv_clahe` (CLAHE + Frangi + ROI Otsu).
fibermorph/analysis/section_pipeline.py	Adds SAM2/watershed segmentation path + extended feature option.
fibermorph/analysis/parallel.py	Formatting-only (line-numbered diff) change.
fibermorph/analysis/curvature_pipeline.py	Adds CLAHE option + extended curvature metrics path.
fibermorph/.gitignore	Formatting-only (line-numbered diff) change.
fibermorph/main.py	Formatting-only (line-numbered diff) change.
fibermorph/init.py	Makes import more resilient; expands exports for v2 APIs.
docs/dependency-audit.md	Formatting-only (line-numbered diff) change.
docs/CONDA_FORGE_SETUP.md	Formatting-only (line-numbered diff) change.
Dockerfile	Adds CPU + GPU targets for containerized Streamlit deployments.
conda-recipe/meta.yaml	Formatting-only currently, but recipe content remains pinned to old version.
CHANGELOG.md	Adds 2.0.0 release notes and new feature list.
.streamlit/config.toml	Formatting-only (line-numbered diff) change.
.python-version	Formatting-only (line-numbered diff) change.
.gitignore	Formatting-only (line-numbered diff) change.
.github/workflows/test.yaml	Switches CI to pip editable install, adds system libs for OpenCV/headless.
.github/workflows/publish.yml	Formatting-only (line-numbered diff) change.
.github/workflows/conventional-prs.yaml	Makes semantic PR check advisory (continue-on-error).
.dockerignore	New docker ignore list to reduce build context.
.devcontainer/devcontainer.json	Formatting-only (line-numbered diff) change.

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

+                    resolution_mu = 1000.0 / resolution
+                    diam = 2.0 * dist_map[rows, cols] / resolution_mu
+                    im_df["diameter_mean_mu"] = float(np.mean(diam))
+                    mean_d = float(np.mean(diam))
+                    im_df["diameter_cv"] = float(np.std(diam) / (mean_d + 1e-10))


+            if "curv_mean_mean" in im_df.columns:
+                curv_vals = im_df["curv_mean_mean"].dropna().values
+            else:
+                curv_vals = np.array([])
+            wc = int(wave_count_fn(curv_vals)) if len(curv_vals) > 0 else 0


+            elif isinstance(result, pd.DataFrame) and not result.empty:
+                row_dict = result.iloc[0].to_dict()
+                row_dict["image_type"]  = image_type
+                row_dict["source_file"] = fname
+                row_dict.update(parse_metadata(fname))
+                rows.append(row_dict)


    "imread",
    "save_image",
    "raw_to_gray",
-    # Utility functions
-    "make_subdirectory",
-    "copy_if_exist",
-    "list_images",
-    "convert",
-    "timing",
    # Demo
    "demo",


+- **`streamlit_app.py`**: Entry point for Streamlit Cloud
+- **`requirements.txt`**: Python dependencies
+- **`.python-version`**: Specifies Python 3.11
+- **`.streamlit/config.toml`**: App configuration (theme, upload limits, etc.)
+- **`packages.txt`**: System-level dependencies for image processing


+RUN python3.11 -m pip install --upgrade pip && \
+    python3.11 -m pip install ".[gui]" && \
+    python3.11 -m pip install torch --index-url https://download.pytorch.org/whl/cu121 && \
+    python3.11 -m pip install git+https://github.com/facebookresearch/segment-anything-2


+{% set name = "fibermorph" %}
+{% set version = "0.3.9" %}


+source:
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/fibermorph-{{ version }}.tar.gz
+  sha256: REPLACE_WITH_SHA256_FROM_PYPI  # Get from https://pypi.org/project/fibermorph/0.3.9/#files


ezhil384 and others added 10 commits March 14, 2026 16:34

Added docker

13b43a9

Updated v2 with SAM

69f15d4

fix: empty packages.txt completely — Streamlit Cloud treats comments …

d0b1ceb

…as package names apt-get was trying to install each word of the comment as a package.

fix: correct segment_section keyword args in GUI helper

eadfc25

app.py was calling segment_section() with sam2_checkpoint=/sam2_cfg= (hair_analysis names) but section_sam2.py defines checkpoint=/model_cfg=.

Merge pull request #2 from ezhil384/copilot/create-new-tests-for-refa…

48dce86

…ctored-version fix(tests): align test suite with refactored v2 API

Merge pull request #1 from ezhil384/feature/v2-enhanced-analysis

d06b3ec

Feature/v2 enhanced analysis

ezhil384 requested review from Copilot and tinalasisi July 3, 2026 19:52

Copilot started reviewing on behalf of ezhil384 July 3, 2026 19:52 View session

Copilot AI reviewed Jul 3, 2026

View reviewed changes

tinalasisi changed the base branch from main to fibermorph-dev July 3, 2026 21:02

tinalasisi merged commit 03c714d into lasisilab:fibermorph-dev Jul 3, 2026
1 check failed

tinalasisi mentioned this pull request Jul 9, 2026

feat: Enhance v2 analysis, fix CI issues, and update dependencies #19

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fibermorph-v2#16

fibermorph-v2#16
tinalasisi merged 10 commits into
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ezhil384 commented Jul 3, 2026

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ezhil384 commented Jul 3, 2026

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