FIX #93: Exported OME tiffs have incorrect channel name data

BodenmillerGroup · Oct 14, 2020 · c7238b7 · c7238b7
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diff --git a/README.md b/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==2.0.1
+pip install imctools==2.1.0
 ```
 In old IMC segmentation pipelines versions 1.x should be used!
 ```

diff --git a/docs/cli.html b/docs/cli.html
@@ -3,7 +3,7 @@
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 <meta charset="utf-8">
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-<meta name="generator" content="pdoc 0.8.4" />
+<meta name="generator" content="pdoc 0.8.5" />
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diff --git a/docs/converters/exportacquisitioncsv.html b/docs/converters/exportacquisitioncsv.html
@@ -3,7 +3,7 @@
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-<meta name="generator" content="pdoc 0.8.4" />
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 <title>imctools.converters.exportacquisitioncsv API documentation</title>
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diff --git a/docs/converters/index.html b/docs/converters/index.html
@@ -3,7 +3,7 @@
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 <meta charset="utf-8">
 <meta name="viewport" content="width=device-width, initial-scale=1, minimum-scale=1" />
-<meta name="generator" content="pdoc 0.8.4" />
+<meta name="generator" content="pdoc 0.8.5" />
 <title>imctools.converters API documentation</title>
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@@ -93,7 +93,7 @@ <h1>Index</h1>
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-<p>Generated by <a href="https://pdoc3.github.io/pdoc"><cite>pdoc</cite> 0.8.4</a>.</p>
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diff --git a/docs/converters/mcdfolder2imcfolder.html b/docs/converters/mcdfolder2imcfolder.html
@@ -3,7 +3,7 @@
 <head>
 <meta charset="utf-8">
 <meta name="viewport" content="width=device-width, initial-scale=1, minimum-scale=1" />
-<meta name="generator" content="pdoc 0.8.4" />
+<meta name="generator" content="pdoc 0.8.5" />
 <title>imctools.converters.mcdfolder2imcfolder API documentation</title>
 <meta name="description" content="" />
 <link rel="preload stylesheet" as="style" href="https://cdnjs.cloudflare.com/ajax/libs/10up-sanitize.css/11.0.1/sanitize.min.css" integrity="sha256-PK9q560IAAa6WVRRh76LtCaI8pjTJ2z11v0miyNNjrs=" crossorigin>
@@ -98,11 +98,13 @@ <h1 class="title">Module <code>imctools.converters.mcdfolder2imcfolder</code></h
     tic = timeit.default_timer()
 
     mcdfolder_to_imcfolder(
-        Path(&#34;/home/anton/Downloads/20170905_Fluidigmworkshopfinal_SEAJa.zip&#34;),
+        # Path(&#34;/home/anton/Downloads/20170905_Fluidigmworkshopfinal_SEAJa.zip&#34;),
+        &#34;/home/anton/Downloads/20170905_Fluidigmworkshopfinal_SEAJa&#34;,
+        # &#34;/home/anton/Documents/merrick/IMC/20200904_MS_XRF_epithelial_panel_4_titration.zip&#34;,
         # &#34;/home/anton/Documents/IMC Workshop 2019/Data/iMC_workshop_2019/20190919_FluidigmBrCa_SE&#34;,
         # &#34;/home/anton/Downloads/test&#34;,
         # &#34;/home/anton/Data/ForAnton/20200123_IMMUcan_reproducibility_day1_sl1_cp_panel_1_1.06.zip&#34;,
-        Path(&#34;/home/anton/Downloads/imc_folder&#34;),
+        Path(&#34;/home/anton/Downloads/imc_folder_v2&#34;),
     )
 
     print(timeit.default_timer() - tic)</code></pre>
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diff --git a/docs/converters/ome2analysis.html b/docs/converters/ome2analysis.html
@@ -3,7 +3,7 @@
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-<meta name="generator" content="pdoc 0.8.4" />
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diff --git a/docs/converters/ome2histocat.html b/docs/converters/ome2histocat.html
@@ -3,7 +3,7 @@
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-<meta name="generator" content="pdoc 0.8.4" />
+<meta name="generator" content="pdoc 0.8.5" />
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@@ -369,7 +369,7 @@ <h1>Index</h1>
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-<p>Generated by <a href="https://pdoc3.github.io/pdoc"><cite>pdoc</cite> 0.8.4</a>.</p>
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diff --git a/docs/converters/v1tov2.html b/docs/converters/v1tov2.html
@@ -3,7 +3,7 @@
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-<meta name="generator" content="pdoc 0.8.4" />
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@@ -243,7 +243,7 @@ <h1>Index</h1>
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-<p>Generated by <a href="https://pdoc3.github.io/pdoc"><cite>pdoc</cite> 0.8.4</a>.</p>
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diff --git a/docs/data/acquisition.html b/docs/data/acquisition.html
@@ -3,7 +3,7 @@
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-<meta name="generator" content="pdoc 0.8.4" />
+<meta name="generator" content="pdoc 0.8.5" />
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@@ -872,7 +872,7 @@ <h4><code><a title="imctools.data.acquisition.AcquisitionDict" href="#imctools.d
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diff --git a/docs/data/acquisitiondata.html b/docs/data/acquisitiondata.html
@@ -3,7 +3,7 @@
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 <meta name="viewport" content="width=device-width, initial-scale=1, minimum-scale=1" />
-<meta name="generator" content="pdoc 0.8.4" />
+<meta name="generator" content="pdoc 0.8.5" />
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@@ -900,7 +900,7 @@ <h4><code><a title="imctools.data.acquisitiondata.AcquisitionData" href="#imctoo
 </nav>
 </main>
 <footer id="footer">
-<p>Generated by <a href="https://pdoc3.github.io/pdoc"><cite>pdoc</cite> 0.8.4</a>.</p>
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diff --git a/docs/data/channel.html b/docs/data/channel.html
@@ -3,7 +3,7 @@
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 <meta charset="utf-8">
 <meta name="viewport" content="width=device-width, initial-scale=1, minimum-scale=1" />
-<meta name="generator" content="pdoc 0.8.4" />
+<meta name="generator" content="pdoc 0.8.5" />
 <title>imctools.data.channel API documentation</title>
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@@ -412,7 +412,7 @@ <h4><code><a title="imctools.data.channel.ChannelDict" href="#imctools.data.chan
 </nav>
 </main>
 <footer id="footer">
-<p>Generated by <a href="https://pdoc3.github.io/pdoc"><cite>pdoc</cite> 0.8.4</a>.</p>
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diff --git a/docs/data/index.html b/docs/data/index.html
@@ -3,7 +3,7 @@
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-<meta name="generator" content="pdoc 0.8.4" />
+<meta name="generator" content="pdoc 0.8.5" />
 <title>imctools.data API documentation</title>
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@@ -94,7 +94,7 @@ <h1>Index</h1>
 </nav>
 </main>
 <footer id="footer">
-<p>Generated by <a href="https://pdoc3.github.io/pdoc"><cite>pdoc</cite> 0.8.4</a>.</p>
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diff --git a/docs/data/panorama.html b/docs/data/panorama.html
@@ -3,7 +3,7 @@
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 <meta charset="utf-8">
 <meta name="viewport" content="width=device-width, initial-scale=1, minimum-scale=1" />
-<meta name="generator" content="pdoc 0.8.4" />
+<meta name="generator" content="pdoc 0.8.5" />
 <title>imctools.data.panorama API documentation</title>
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@@ -486,7 +486,7 @@ <h4><code><a title="imctools.data.panorama.PanoramaDict" href="#imctools.data.pa
 </nav>
 </main>
 <footer id="footer">
-<p>Generated by <a href="https://pdoc3.github.io/pdoc"><cite>pdoc</cite> 0.8.4</a>.</p>
+<p>Generated by <a href="https://pdoc3.github.io/pdoc"><cite>pdoc</cite> 0.8.5</a>.</p>
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diff --git a/docs/data/session.html b/docs/data/session.html
@@ -3,7 +3,7 @@
 <head>
 <meta charset="utf-8">
 <meta name="viewport" content="width=device-width, initial-scale=1, minimum-scale=1" />
-<meta name="generator" content="pdoc 0.8.4" />
+<meta name="generator" content="pdoc 0.8.5" />
 <title>imctools.data.session API documentation</title>
 <meta name="description" content="" />
 <link rel="preload stylesheet" as="style" href="https://cdnjs.cloudflare.com/ajax/libs/10up-sanitize.css/11.0.1/sanitize.min.css" integrity="sha256-PK9q560IAAa6WVRRh76LtCaI8pjTJ2z11v0miyNNjrs=" crossorigin>
@@ -41,7 +41,7 @@ <h1 class="title">Module <code>imctools.data.session</code></h1>
 from imctools.data.channel import Channel, ChannelDict
 from imctools.data.panorama import Panorama, PanoramaDict
 from imctools.data.slide import Slide, SlideDict
-from imctools.io.utils import META_CSV_SUFFIX
+from imctools.io.utils import META_CSV_SUFFIX, sort_acquisition_channels
 
 if sys.version_info &gt;= (3, 8):
     from typing import TypedDict  # pylint: disable=no-name-in-module
@@ -217,6 +217,9 @@ <h1 class="title">Module <code>imctools.data.session</code></h1>
             acquisition.channels[channel.id] = channel
             session.channels[channel.id] = channel
 
+        # Sort acquisitions channels by ORDER_NUMBER
+        sort_acquisition_channels(session)
+
         return session
 
     @property
@@ -236,7 +239,9 @@ <h1 class="title">Module <code>imctools.data.session</code></h1>
     import timeit
 
     tic = timeit.default_timer()
-    session = Session.load(&#34;/home/anton/Downloads/imc_from_mcd/20190919_FluidigmBrCa_SE_session.json&#34;)
+    session = Session.load(
+        &#34;/home/anton/Downloads/imc_folder_v2/20170905_Fluidigmworkshopfinal_SEAJa/20170905_Fluidigmworkshopfinal_SEAJa_session.json&#34;
+    )
     print(timeit.default_timer() - tic)</code></pre>
 </details>
 </section>
@@ -428,6 +433,9 @@ <h2 id="parameters">Parameters</h2>
             acquisition.channels[channel.id] = channel
             session.channels[channel.id] = channel
 
+        # Sort acquisitions channels by ORDER_NUMBER
+        sort_acquisition_channels(session)
+
         return session
 
     @property
@@ -685,7 +693,7 @@ <h4><code><a title="imctools.data.session.SessionDict" href="#imctools.data.sess
 </nav>
 </main>
 <footer id="footer">
-<p>Generated by <a href="https://pdoc3.github.io/pdoc"><cite>pdoc</cite> 0.8.4</a>.</p>
+<p>Generated by <a href="https://pdoc3.github.io/pdoc"><cite>pdoc</cite> 0.8.5</a>.</p>
 </footer>
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diff --git a/docs/data/slide.html b/docs/data/slide.html
@@ -3,7 +3,7 @@
 <head>
 <meta charset="utf-8">
 <meta name="viewport" content="width=device-width, initial-scale=1, minimum-scale=1" />
-<meta name="generator" content="pdoc 0.8.4" />
+<meta name="generator" content="pdoc 0.8.5" />
 <title>imctools.data.slide API documentation</title>
 <meta name="description" content="" />
 <link rel="preload stylesheet" as="style" href="https://cdnjs.cloudflare.com/ajax/libs/10up-sanitize.css/11.0.1/sanitize.min.css" integrity="sha256-PK9q560IAAa6WVRRh76LtCaI8pjTJ2z11v0miyNNjrs=" crossorigin>
@@ -491,7 +491,7 @@ <h4><code><a title="imctools.data.slide.SlideDict" href="#imctools.data.slide.Sl
 </nav>
 </main>
 <footer id="footer">
-<p>Generated by <a href="https://pdoc3.github.io/pdoc"><cite>pdoc</cite> 0.8.4</a>.</p>
+<p>Generated by <a href="https://pdoc3.github.io/pdoc"><cite>pdoc</cite> 0.8.5</a>.</p>
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diff --git a/docs/index.html b/docs/index.html
@@ -3,7 +3,7 @@
 <head>
 <meta charset="utf-8">
 <meta name="viewport" content="width=device-width, initial-scale=1, minimum-scale=1" />
-<meta name="generator" content="pdoc 0.8.4" />
+<meta name="generator" content="pdoc 0.8.5" />
 <title>imctools API documentation</title>
 <meta name="description" content="imctools …" />
 <link rel="preload stylesheet" as="style" href="https://cdnjs.cloudflare.com/ajax/libs/10up-sanitize.css/11.0.1/sanitize.min.css" integrity="sha256-PK9q560IAAa6WVRRh76LtCaI8pjTJ2z11v0miyNNjrs=" crossorigin>
@@ -49,15 +49,15 @@ <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==2.0.1
+<pre><code>pip install imctools==2.1.0
 </code></pre>
 <p>In old IMC segmentation pipelines versions 1.x should be used!</p>
 <pre><code>pip install imctools==1.0.8
 </code></pre>
 <h2 id="usage-of-version-2x">Usage of version 2.x</h2>
 <p><code><a title="imctools" href="#imctools">imctools</a></code> is often used from Jupyter as part of the pre-processing pipeline, mainly using the <strong>converters</strong> wrapper functions. Please check the <a href="https://github.com/BodenmillerGroup/ImcSegmentationPipeline/blob/development/scripts/imc_preprocessing.ipynb">following example</a> as a template.</p>
 <p>Further <code><a title="imctools" href="#imctools">imctools</a></code> can be directly used as a module:</p>
-<pre><code class="python">from imctools.io.mcd.mcdparser import McdParser
+<pre><code class="language-python">from imctools.io.mcd.mcdparser import McdParser
 
 fn_mcd = &quot;/home/vitoz/Data/varia/201708_instrument_comp/mcd/20170815_imccomp_zoidberg_conc5_acm1.mcd&quot;
 
@@ -93,7 +93,7 @@ <h2 id="usage-of-version-2x">Usage of version 2.x</h2>
 parser.close()
 </code></pre>
 <h3 id="usage-of-previous-version-1x">Usage of previous version 1.x</h3>
-<pre><code class="python">import imctools.io.mcdparser as mcdparser
+<pre><code class="language-python">import imctools.io.mcdparser as mcdparser
 import imctools.io.txtparser as txtparser
 import imctools.io.ometiffparser as omeparser
 import imctools.io.mcdxmlparser as meta
@@ -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;2.0.1&#34;</code></pre>
+__version__ = &#34;2.1.0&#34;</code></pre>
 </details>
 </section>
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@@ -200,7 +200,7 @@ <h1>Index</h1>
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 <footer id="footer">
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