Prevent crash on corrupted MCD acquisitions in order to keep valid ones.

CHANGELOG.md

@@ -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).
 
+## [2.1.2] - 2021-01-21
+- Prevent crash on corrupted MCD acquisitions in order to keep valid ones
+
 ## [2.1.1] - 2021-01-20
 - Update `xtiff` package
 - FIX: Wrong ROI coordinates for new Fluidigm software versions #104

README.md

@@ -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==2.1.1
+pip install imctools==2.1.2
 ```
 In old IMC segmentation pipelines versions 1.x should be used!
 ```

docs/index.html

@@ -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==2.1.1
+<pre><code>pip install imctools==2.1.2
 </code></pre>
 <p>In old IMC segmentation pipelines versions 1.x should be used!</p>
 <pre><code>pip install imctools==1.0.8

docs/io/mcd/mcdparser.html

@@ -89,11 +89,11 @@ <h1 class="title">Module <code>imctools.io.mcd.mcdparser</code></h1>
         if acquisition is None:
             return None
         data = self._get_acquisition_raw_data(acquisition)
-        if data is not None:
+        try:
             image_data = reshape_long_2_cyx(data, is_sorted=True)
             # Drop first three channels X, Y, Z
             image_data = image_data[3:]
-        else:
+        except:
             image_data = None
             acquisition.is_valid = False
             logger.warning(f&#34;Error reading MCD acquisition: {acquisition_id}&#34;)
@@ -393,11 +393,11 @@ <h2 class="section-title" id="header-classes">Classes</h2>
         if acquisition is None:
             return None
         data = self._get_acquisition_raw_data(acquisition)
-        if data is not None:
+        try:
             image_data = reshape_long_2_cyx(data, is_sorted=True)
             # Drop first three channels X, Y, Z
             image_data = image_data[3:]
-        else:
+        except:
             image_data = None
             acquisition.is_valid = False
             logger.warning(f&#34;Error reading MCD acquisition: {acquisition_id}&#34;)
@@ -693,11 +693,11 @@ <h3>Methods</h3>
     if acquisition is None:
         return None
     data = self._get_acquisition_raw_data(acquisition)
-    if data is not None:
+    try:
         image_data = reshape_long_2_cyx(data, is_sorted=True)
         # Drop first three channels X, Y, Z
         image_data = image_data[3:]
-    else:
+    except:
         image_data = None
         acquisition.is_valid = False
         logger.warning(f&#34;Error reading MCD acquisition: {acquisition_id}&#34;)

imctools/io/mcd/mcdparser.py

@@ -61,11 +61,11 @@ def get_acquisition_data(self, acquisition_id: int):
         if acquisition is None:
             return None
         data = self._get_acquisition_raw_data(acquisition)
-        if data is not None:
+        try:
             image_data = reshape_long_2_cyx(data, is_sorted=True)
             # Drop first three channels X, Y, Z
             image_data = image_data[3:]
-        else:
+        except:
             image_data = None
             acquisition.is_valid = False
             logger.warning(f"Error reading MCD acquisition: {acquisition_id}")

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "imctools"
-version = "2.1.1"
+version = "2.1.2"
 description = "Tools to handle Fluidigm IMC data"
 license = "MIT"
 authors = ["Vito Zanotelli <[email protected]>", "Anton Rau <[email protected]>"]

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.1.1
+current_version = 2.1.2
 commit = False
 tag = False