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Proper parsing of invalid MCD files when some acquisitions offset are…
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… outside the file's size.
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plankter committed Feb 1, 2021
1 parent 959ad00 commit 00a3242
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -5,6 +5,9 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [2.1.4] - 2021-02-01
- Proper parsing of invalid MCD files when some acquisitions offset are outside the file's size

## [2.1.3] - 2021-01-21
- Option to force usage of TXT files in `mcdfolder_to_imcfolder` when dealing with partially corrupted MCD files

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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -32,7 +32,7 @@ Version 1.x documentation (deprecated): https://imctools.readthedocs.io

Preferable way to install `imctools` is via official PyPI registry. Please define package version explicitly in order to avoid incompatibilities between v1.x and v2.x versions:
```
pip install imctools==2.1.3
pip install imctools==2.1.4
```
In old IMC segmentation pipelines versions 1.x should be used!
```
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4 changes: 2 additions & 2 deletions docs/index.html
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Expand Up @@ -49,7 +49,7 @@ <h2 id="prerequisites">Prerequisites</h2>
</ul>
<h2 id="installation">Installation</h2>
<p>Preferable way to install <code><a title="imctools" href="#imctools">imctools</a></code> is via official PyPI registry. Please define package version explicitly in order to avoid incompatibilities between v1.x and v2.x versions:</p>
<pre><code>pip install imctools==2.1.3
<pre><code>pip install imctools==2.1.4
</code></pre>
<p>In old IMC segmentation pipelines versions 1.x should be used!</p>
<pre><code>pip install imctools==1.0.8
Expand Down Expand Up @@ -140,7 +140,7 @@ <h3 id="usage-of-previous-version-1x">Usage of previous version 1.x</h3>

__author__ = &#34;&#34;&#34;Vito Zanotelli, Anton Rau&#34;&#34;&#34;
__email__ = &#34;[email protected], [email protected]&#34;
__version__ = &#34;2.1.3&#34;</code></pre>
__version__ = &#34;2.1.4&#34;</code></pre>
</details>
</section>
<section>
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6 changes: 3 additions & 3 deletions docs/io/mcd/mcdparser.html
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Expand Up @@ -88,8 +88,8 @@ <h1 class="title">Module <code>imctools.io.mcd.mcdparser</code></h1>
acquisition = self.session.acquisitions.get(acquisition_id)
if acquisition is None:
return None
data = self._get_acquisition_raw_data(acquisition)
try:
data = self._get_acquisition_raw_data(acquisition)
image_data = reshape_long_2_cyx(data, is_sorted=True)
# Drop first three channels X, Y, Z
image_data = image_data[3:]
Expand Down Expand Up @@ -392,8 +392,8 @@ <h2 class="section-title" id="header-classes">Classes</h2>
acquisition = self.session.acquisitions.get(acquisition_id)
if acquisition is None:
return None
data = self._get_acquisition_raw_data(acquisition)
try:
data = self._get_acquisition_raw_data(acquisition)
image_data = reshape_long_2_cyx(data, is_sorted=True)
# Drop first three channels X, Y, Z
image_data = image_data[3:]
Expand Down Expand Up @@ -692,8 +692,8 @@ <h3>Methods</h3>
acquisition = self.session.acquisitions.get(acquisition_id)
if acquisition is None:
return None
data = self._get_acquisition_raw_data(acquisition)
try:
data = self._get_acquisition_raw_data(acquisition)
image_data = reshape_long_2_cyx(data, is_sorted=True)
# Drop first three channels X, Y, Z
image_data = image_data[3:]
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2 changes: 1 addition & 1 deletion imctools/__init__.py
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Expand Up @@ -6,4 +6,4 @@

__author__ = """Vito Zanotelli, Anton Rau"""
__email__ = "[email protected], [email protected]"
__version__ = "2.1.3"
__version__ = "2.1.4"
2 changes: 1 addition & 1 deletion imctools/io/mcd/mcdparser.py
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Expand Up @@ -60,8 +60,8 @@ def get_acquisition_data(self, acquisition_id: int):
acquisition = self.session.acquisitions.get(acquisition_id)
if acquisition is None:
return None
data = self._get_acquisition_raw_data(acquisition)
try:
data = self._get_acquisition_raw_data(acquisition)
image_data = reshape_long_2_cyx(data, is_sorted=True)
# Drop first three channels X, Y, Z
image_data = image_data[3:]
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2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"

[tool.poetry]
name = "imctools"
version = "2.1.3"
version = "2.1.4"
description = "Tools to handle Fluidigm IMC data"
license = "MIT"
authors = ["Vito Zanotelli <[email protected]>", "Anton Rau <[email protected]>"]
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2 changes: 1 addition & 1 deletion setup.cfg
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@@ -1,5 +1,5 @@
[bumpversion]
current_version = 2.1.3
current_version = 2.1.4
commit = False
tag = False

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