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Fix bad NA value Issue #41

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merged 4 commits into from
Aug 5, 2022
Merged

Fix bad NA value Issue #41

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e4192ee
Fix incorrect NA replacement value
Eve-ning Aug 5, 2022
4ad34f0
Remove redundant test
Eve-ning Aug 5, 2022
ab4f803
Use nansum for handling nans
Eve-ning Aug 5, 2022
ac5acf2
Update changelog for this MR
Eve-ning Aug 5, 2022
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5 changes: 4 additions & 1 deletion docs/_sources/changelog.md.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@
- Reduces duplicate code for handling NumPy and CuPy arrays conditionally.
- [Merged PR 36](https://github.com/Eve-ning/glcm-cupy/pull/36)
- Implement NaN Handling by ignoring contribution to GLCM

## 1.9

- [Merged PR 10](https://github.com/Eve-ning/glcm-cupy/pull/10)
Expand All @@ -40,6 +40,9 @@
- Fix `test_from_2d_image` failing due to missing 3rd dimension
- Remove `test_image_tiff` as it's redundant
- Fix reference `GLCM._binner` to `binner` in `utils`
- [Merged PR 41](https://github.com/Eve-ning/glcm-cupy/pull/41)
- Resolved issue where NA replacement value was incorrectly set to `bin_from`
- Resolved issue where NA summing used `.sum` instead of `np.nansum`

## 1.8

Expand Down
6 changes: 6 additions & 0 deletions docs/changelog.html
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Original file line number Diff line number Diff line change
Expand Up @@ -248,6 +248,12 @@ <h2>1.9<a class="headerlink" href="#id2" title="Permalink to this heading">¶</a
<li><p>Fix reference <code class="docutils literal notranslate"><span class="pre">GLCM._binner</span></code> to <code class="docutils literal notranslate"><span class="pre">binner</span></code> in <code class="docutils literal notranslate"><span class="pre">utils</span></code></p></li>
</ul>
</li>
<li><p><a class="reference external" href="https://github.com/Eve-ning/glcm-cupy/pull/41">Merged PR 41</a></p>
<ul>
<li><p>Resolved issue where NA replacement value was incorrectly set to <code class="docutils literal notranslate"><span class="pre">bin_from</span></code></p></li>
<li><p>Resolved issue where NA summing used <code class="docutils literal notranslate"><span class="pre">.sum</span></code> instead of <code class="docutils literal notranslate"><span class="pre">np.nansum</span></code></p></li>
</ul>
</li>
</ul>
</div>
<div class="section" id="id3">
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2 changes: 1 addition & 1 deletion docs/searchindex.js
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6 changes: 3 additions & 3 deletions glcm_cupy/glcm_base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -121,7 +121,7 @@ def glcm_cells(self, im: cp.ndarray) -> float:
@property
def nan_replacement(self):
""" Replacement Value for NaN """
return self.bin_from
return self.bin_to

def run(self, im: ndarray):
""" Executes running GLCM. Returns the GLCM Feature array
Expand Down Expand Up @@ -340,8 +340,8 @@ def glcm_ij(self,
self.ar_features,
True)
)
self.ar_glcm /= self.ar_glcm.sum(
axis=(1, 2)
self.ar_glcm /= np.nansum(
self.ar_glcm, axis=(1, 2)
)[..., np.newaxis, np.newaxis]
if self.do_stage(0): self.glcm_feature_kernel_0(**feature_args)
if self.do_stage(1): self.glcm_feature_kernel_1(**feature_args)
Expand Down
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5 changes: 4 additions & 1 deletion sphinx/build/html/_sources/changelog.md.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@
- Reduces duplicate code for handling NumPy and CuPy arrays conditionally.
- [Merged PR 36](https://github.com/Eve-ning/glcm-cupy/pull/36)
- Implement NaN Handling by ignoring contribution to GLCM

## 1.9

- [Merged PR 10](https://github.com/Eve-ning/glcm-cupy/pull/10)
Expand All @@ -40,6 +40,9 @@
- Fix `test_from_2d_image` failing due to missing 3rd dimension
- Remove `test_image_tiff` as it's redundant
- Fix reference `GLCM._binner` to `binner` in `utils`
- [Merged PR 41](https://github.com/Eve-ning/glcm-cupy/pull/41)
- Resolved issue where NA replacement value was incorrectly set to `bin_from`
- Resolved issue where NA summing used `.sum` instead of `np.nansum`

## 1.8

Expand Down
6 changes: 6 additions & 0 deletions sphinx/build/html/changelog.html
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Original file line number Diff line number Diff line change
Expand Up @@ -248,6 +248,12 @@ <h2>1.9<a class="headerlink" href="#id2" title="Permalink to this heading">¶</a
<li><p>Fix reference <code class="docutils literal notranslate"><span class="pre">GLCM._binner</span></code> to <code class="docutils literal notranslate"><span class="pre">binner</span></code> in <code class="docutils literal notranslate"><span class="pre">utils</span></code></p></li>
</ul>
</li>
<li><p><a class="reference external" href="https://github.com/Eve-ning/glcm-cupy/pull/41">Merged PR 41</a></p>
<ul>
<li><p>Resolved issue where NA replacement value was incorrectly set to <code class="docutils literal notranslate"><span class="pre">bin_from</span></code></p></li>
<li><p>Resolved issue where NA summing used <code class="docutils literal notranslate"><span class="pre">.sum</span></code> instead of <code class="docutils literal notranslate"><span class="pre">np.nansum</span></code></p></li>
</ul>
</li>
</ul>
</div>
<div class="section" id="id3">
Expand Down
2 changes: 1 addition & 1 deletion sphinx/build/html/searchindex.js
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Large diffs are not rendered by default.

5 changes: 4 additions & 1 deletion sphinx/src/changelog.md
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@
- Reduces duplicate code for handling NumPy and CuPy arrays conditionally.
- [Merged PR 36](https://github.com/Eve-ning/glcm-cupy/pull/36)
- Implement NaN Handling by ignoring contribution to GLCM

## 1.9

- [Merged PR 10](https://github.com/Eve-ning/glcm-cupy/pull/10)
Expand All @@ -40,6 +40,9 @@
- Fix `test_from_2d_image` failing due to missing 3rd dimension
- Remove `test_image_tiff` as it's redundant
- Fix reference `GLCM._binner` to `binner` in `utils`
- [Merged PR 41](https://github.com/Eve-ning/glcm-cupy/pull/41)
- Resolved issue where NA replacement value was incorrectly set to `bin_from`
- Resolved issue where NA summing used `.sum` instead of `np.nansum`

## 1.8

Expand Down
7 changes: 0 additions & 7 deletions tests/integration_tests/test_padding.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,10 +56,3 @@ def test_signature_match():
fn = dict(inspect.signature(glcm).parameters)
del fn['im']
assert cls == fn

def test_padding():
""" Tests if class & function signatures match """
cls = dict(inspect.signature(GLCM).parameters)
fn = dict(inspect.signature(glcm).parameters)
del fn['im']
assert cls == fn