sem2surface 0.2.1__tar.gz → 0.2.2__tar.gz

{sem2surface-0.2.1/src/sem2surface.egg-info → sem2surface-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sem2surface
-Version: 0.2.1
+Version: 0.2.2
 Summary: 3D surface reconstruction from multi-detector SEM/BSE images
 Author: Vladislav A. Yastrebov
 License-Expression: BSD-3-Clause
@@ -186,6 +186,12 @@ decomposition, Radon search, and oriented gradients.
 When timestamps are disabled, an existing output with the same name is replaced.
 Choose a dedicated output folder or enable timestamps when results must be kept.
 
+For TIFF acquisitions, `sem2surface` automatically removes a microscope
+annotation footer when it detects a nearly uniform bright separator followed by
+a statistically distinct lower band. The detector works with both 8-bit Zeiss
+and 16-bit FEI exports, leaves footer-free images unchanged, and records every
+detected crop in the processing log.
+
 ## Reference examples and scaling
 
 The [examples directory](https://github.com/vyastreb/sem2surface/tree/master/examples)
@@ -206,6 +212,15 @@ python examples/Surface_1/test_without_gui.py
 <!-- PyPI cannot resolve repository-relative images. Keep this absolute URL. -->
 ![Reconstruction of the indented surface](https://raw.githubusercontent.com/vyastreb/sem2surface/master/img/indent_superposition.jpg)
 
+## Changes in 0.2.2
+
+- Replaced the historical hard-coded footer threshold with bit-depth-independent
+  SEM annotation-band detection.
+- Added safeguards against cropping isolated bright lines in specimen data.
+- Added per-image logging of detected footers and removed row counts.
+- Added regression coverage for 8-bit Zeiss, 16-bit FEI, footer-free, and
+  isolated-line images.
+
 ## Development
 
 Create an isolated environment and install the editable project with its test
@@ -240,7 +255,7 @@ For a first trial, create a separate account and API token on
 version:
 
 ```bash
-python -m twine upload --repository testpypi dist/sem2surface-0.2.1*
+python -m twine upload --repository testpypi dist/sem2surface-0.2.2*
 ```
 
 When prompted, use `__token__` as the username and the complete TestPyPI token,
@@ -248,7 +263,7 @@ including its `pypi-` prefix, as the password. Test the uploaded wheel in a new
 environment without resolving dependencies from TestPyPI:
 
 ```bash
-python -m pip install --index-url https://test.pypi.org/simple/ --no-deps sem2surface==0.2.1
+python -m pip install --index-url https://test.pypi.org/simple/ --no-deps sem2surface==0.2.2
 sem2surface --version
 ```
 
@@ -256,7 +271,7 @@ For the real release, create a PyPI account and API token at
 [pypi.org](https://pypi.org/), then run:
 
 ```bash
-python -m twine upload dist/sem2surface-0.2.1*
+python -m twine upload dist/sem2surface-0.2.2*
 ```
 
 PyPI and TestPyPI use separate accounts and tokens. Never commit a token or put

{sem2surface-0.2.1 → sem2surface-0.2.2}/README.md

@@ -147,6 +147,12 @@ decomposition, Radon search, and oriented gradients.
 When timestamps are disabled, an existing output with the same name is replaced.
 Choose a dedicated output folder or enable timestamps when results must be kept.
 
+For TIFF acquisitions, `sem2surface` automatically removes a microscope
+annotation footer when it detects a nearly uniform bright separator followed by
+a statistically distinct lower band. The detector works with both 8-bit Zeiss
+and 16-bit FEI exports, leaves footer-free images unchanged, and records every
+detected crop in the processing log.
+
 ## Reference examples and scaling
 
 The [examples directory](https://github.com/vyastreb/sem2surface/tree/master/examples)
@@ -167,6 +173,15 @@ python examples/Surface_1/test_without_gui.py
 <!-- PyPI cannot resolve repository-relative images. Keep this absolute URL. -->
 ![Reconstruction of the indented surface](https://raw.githubusercontent.com/vyastreb/sem2surface/master/img/indent_superposition.jpg)
 
+## Changes in 0.2.2
+
+- Replaced the historical hard-coded footer threshold with bit-depth-independent
+  SEM annotation-band detection.
+- Added safeguards against cropping isolated bright lines in specimen data.
+- Added per-image logging of detected footers and removed row counts.
+- Added regression coverage for 8-bit Zeiss, 16-bit FEI, footer-free, and
+  isolated-line images.
+
 ## Development
 
 Create an isolated environment and install the editable project with its test
@@ -201,7 +216,7 @@ For a first trial, create a separate account and API token on
 version:
 
 ```bash
-python -m twine upload --repository testpypi dist/sem2surface-0.2.1*
+python -m twine upload --repository testpypi dist/sem2surface-0.2.2*
 ```
 
 When prompted, use `__token__` as the username and the complete TestPyPI token,
@@ -209,7 +224,7 @@ including its `pypi-` prefix, as the password. Test the uploaded wheel in a new
 environment without resolving dependencies from TestPyPI:
 
 ```bash
-python -m pip install --index-url https://test.pypi.org/simple/ --no-deps sem2surface==0.2.1
+python -m pip install --index-url https://test.pypi.org/simple/ --no-deps sem2surface==0.2.2
 sem2surface --version
 ```
 
@@ -217,7 +232,7 @@ For the real release, create a PyPI account and API token at
 [pypi.org](https://pypi.org/), then run:
 
 ```bash
-python -m twine upload dist/sem2surface-0.2.1*
+python -m twine upload dist/sem2surface-0.2.2*
 ```
 
 PyPI and TestPyPI use separate accounts and tokens. Never commit a token or put

{sem2surface-0.2.1 → sem2surface-0.2.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "sem2surface"
-version = "0.2.1"
+version = "0.2.2"
 description = "3D surface reconstruction from multi-detector SEM/BSE images"
 readme = "README.md"
 requires-python = ">=3.10"

{sem2surface-0.2.1 → sem2surface-0.2.2/src/sem2surface.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sem2surface
-Version: 0.2.1
+Version: 0.2.2
 Summary: 3D surface reconstruction from multi-detector SEM/BSE images
 Author: Vladislav A. Yastrebov
 License-Expression: BSD-3-Clause
@@ -186,6 +186,12 @@ decomposition, Radon search, and oriented gradients.
 When timestamps are disabled, an existing output with the same name is replaced.
 Choose a dedicated output folder or enable timestamps when results must be kept.
 
+For TIFF acquisitions, `sem2surface` automatically removes a microscope
+annotation footer when it detects a nearly uniform bright separator followed by
+a statistically distinct lower band. The detector works with both 8-bit Zeiss
+and 16-bit FEI exports, leaves footer-free images unchanged, and records every
+detected crop in the processing log.
+
 ## Reference examples and scaling
 
 The [examples directory](https://github.com/vyastreb/sem2surface/tree/master/examples)
@@ -206,6 +212,15 @@ python examples/Surface_1/test_without_gui.py
 <!-- PyPI cannot resolve repository-relative images. Keep this absolute URL. -->
 ![Reconstruction of the indented surface](https://raw.githubusercontent.com/vyastreb/sem2surface/master/img/indent_superposition.jpg)
 
+## Changes in 0.2.2
+
+- Replaced the historical hard-coded footer threshold with bit-depth-independent
+  SEM annotation-band detection.
+- Added safeguards against cropping isolated bright lines in specimen data.
+- Added per-image logging of detected footers and removed row counts.
+- Added regression coverage for 8-bit Zeiss, 16-bit FEI, footer-free, and
+  isolated-line images.
+
 ## Development
 
 Create an isolated environment and install the editable project with its test
@@ -240,7 +255,7 @@ For a first trial, create a separate account and API token on
 version:
 
 ```bash
-python -m twine upload --repository testpypi dist/sem2surface-0.2.1*
+python -m twine upload --repository testpypi dist/sem2surface-0.2.2*
 ```
 
 When prompted, use `__token__` as the username and the complete TestPyPI token,
@@ -248,7 +263,7 @@ including its `pypi-` prefix, as the password. Test the uploaded wheel in a new
 environment without resolving dependencies from TestPyPI:
 
 ```bash
-python -m pip install --index-url https://test.pypi.org/simple/ --no-deps sem2surface==0.2.1
+python -m pip install --index-url https://test.pypi.org/simple/ --no-deps sem2surface==0.2.2
 sem2surface --version
 ```
 
@@ -256,7 +271,7 @@ For the real release, create a PyPI account and API token at
 [pypi.org](https://pypi.org/), then run:
 
 ```bash
-python -m twine upload dist/sem2surface-0.2.1*
+python -m twine upload dist/sem2surface-0.2.2*
 ```
 
 PyPI and TestPyPI use separate accounts and tokens. Never commit a token or put

{sem2surface-0.2.1 → sem2surface-0.2.2}/src/sem2surface.py

@@ -23,7 +23,7 @@ from scipy.ndimage import gaussian_filter
 from skimage.transform import radon
 
 
-__version__ = "0.2.1"
+__version__ = "0.2.2"
 DEFAULT_PIXEL_SIZE = 1e-6
 _PIXEL_WIDTH_TAGS = ("PixelWidth=", "Image Pixel Size =")
 
@@ -261,6 +261,49 @@ def _read_image(path: Path) -> np.ndarray:
     return np.asarray(convert_to_grayscale(array), dtype=np.float64)
 
 
+def _find_sem_data_rows(image: np.ndarray) -> int:
+    """Return the number of rows above a SEM annotation footer.
+
+    FEI and Zeiss exports use different bit depths and footer layouts, but both
+    place a nearly uniform bright separator near the bottom of the image.  A
+    separator is accepted only when the pixels below it have a substantially
+    different median intensity, which avoids treating an isolated bright line
+    in the specimen as a footer.
+    """
+    array = np.asarray(image, dtype=np.float64)
+    if array.ndim != 2:
+        raise ValueError("Footer detection requires a two-dimensional image")
+    rows, columns = array.shape
+    if rows < 16 or columns < 16:
+        return rows
+
+    finite = array[np.isfinite(array)]
+    if finite.size == 0:
+        return rows
+    low, high = np.percentile(finite, (0.1, 99.9))
+    intensity_span = float(high - low)
+    if not np.isfinite(intensity_span) or intensity_span <= 0:
+        return rows
+
+    # The 3% tolerance includes FEI separator values (64512) when a few
+    # saturated specimen pixels raise the 99.9th percentile to 65535.
+    bright_threshold = high - 0.03 * intensity_span
+    bright_fraction = np.mean(array >= bright_threshold, axis=1)
+    first_candidate = max(1, int(np.ceil(0.5 * rows)))
+    minimum_footer_rows = max(4, int(np.ceil(0.01 * rows)))
+    candidate_stop = rows - minimum_footer_rows + 1
+
+    for row in range(first_candidate, candidate_stop):
+        if bright_fraction[row] < 0.98 or bright_fraction[row - 1] >= 0.5:
+            continue
+        preceding_rows = min(64, row)
+        specimen_median = float(np.nanmedian(array[row - preceding_rows : row]))
+        footer_median = float(np.nanmedian(array[row:]))
+        if abs(footer_median - specimen_median) >= 0.10 * intensity_span:
+            return row
+    return rows
+
+
 def _plot_image_decomposition(
     imgs: np.ndarray,
     intensity: np.ndarray,
@@ -537,16 +580,16 @@ def _construct_surface(
     if len(widths) != 1:
         raise ValueError("All detector images must have the same width")
 
-    # Preserve the footer marker used by the reference data while applying the
-    # same crop safely to every detector image.
-    crop_rows: list[int] = []
-    for image in images:
-        crop = image.shape[0]
-        row_means = np.mean(image, axis=1)
-        marker = np.flatnonzero(np.abs(row_means[1:] - 1437.0) < 2)
-        if marker.size:
-            crop = max(1, int(marker[0]))
-        crop_rows.append(crop)
+    # Detect each footer independently, then apply the smallest common crop so
+    # all detector images retain identical dimensions.
+    crop_rows = [_find_sem_data_rows(image) for image in images]
+    for path, image, crop in zip(paths, images, crop_rows):
+        if crop < image.shape[0]:
+            log(
+                log_file,
+                f"SEM annotation footer detected in {path.name}: "
+                f"removed {image.shape[0] - crop} rows",
+            )
     cut_y = min(crop_rows)
     if cut_y < 2:
         raise ValueError("Automatic footer detection left too little image data")

{sem2surface-0.2.1 → sem2surface-0.2.2}/src/sem2surface_cli.py

@@ -3,15 +3,10 @@
 from __future__ import annotations
 
 import argparse
-from importlib.metadata import PackageNotFoundError, version
 from pathlib import Path
 from typing import Sequence
 
-
-try:
-    VERSION = version("sem2surface")
-except PackageNotFoundError:  # Running directly from an unpacked source tree.
-    VERSION = "0.2.1"
+from sem2surface import __version__ as VERSION
 
 
 def build_parser() -> argparse.ArgumentParser:

{sem2surface-0.2.1 → sem2surface-0.2.2}/tests/test_cli.py

@@ -8,7 +8,7 @@ def test_cli_exposes_version(capsys):
     with pytest.raises(SystemExit) as raised:
         parser.parse_args(["--version"])
     assert raised.value.code == 0
-    assert "0.2.1" in capsys.readouterr().out
+    assert "0.2.2" in capsys.readouterr().out
 
 
 def test_cli_requires_three_images(capsys):

{sem2surface-0.2.1 → sem2surface-0.2.2}/tests/test_core.py

@@ -4,6 +4,7 @@ import numpy as np
 import pytest
 
 from sem2surface import (
+    _find_sem_data_rows,
     compute_image_gradients,
     construct_surface,
     convert_to_grayscale,
@@ -58,3 +59,40 @@ def test_caller_owned_log_is_not_closed():
     with pytest.raises(ValueError):
         construct_surface([], log_file=stream)
     assert not stream.closed
+
+
+def test_footer_detection_handles_fei_16_bit_separator():
+    rng = np.random.default_rng(3)
+    image = rng.integers(28000, 48000, size=(80, 64), dtype=np.uint16)
+    image.flat[:12] = 65535  # Saturated specimen pixels above the separator.
+    image[64] = 64512
+    image[65:] = 1024
+    image[68:76:3, 5:59:7] = 64512
+    image[-1] = 64512
+
+    assert _find_sem_data_rows(image) == 64
+
+
+def test_footer_detection_handles_zeiss_8_bit_band():
+    rng = np.random.default_rng(5)
+    image = rng.integers(90, 190, size=(120, 64), dtype=np.uint8)
+    image[101] = 0
+    image[102:] = 255
+    image[105:117:3, 4:60:6] = 0
+
+    assert _find_sem_data_rows(image) == 102
+
+
+def test_footer_detection_leaves_footer_free_image_unchanged():
+    rng = np.random.default_rng(7)
+    image = rng.integers(40, 220, size=(120, 64), dtype=np.uint8)
+
+    assert _find_sem_data_rows(image) == image.shape[0]
+
+
+def test_footer_detection_ignores_isolated_bright_specimen_line():
+    rng = np.random.default_rng(11)
+    image = rng.integers(80, 180, size=(120, 64), dtype=np.uint8)
+    image[75] = 255
+
+    assert _find_sem_data_rows(image) == image.shape[0]