From 85c968d766eed5d9bb7ec4e7d9fad00b288156b8 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Wed, 25 Sep 2024 17:34:43 +0200
Subject: [PATCH 01/15] update dependency versions

---
 tools/idr_download/idr_download_by_ids.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/idr_download/idr_download_by_ids.xml b/tools/idr_download/idr_download_by_ids.xml
index 26af1ddf947..5e3395043dc 100644
--- a/tools/idr_download/idr_download_by_ids.xml
+++ b/tools/idr_download/idr_download_by_ids.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="idr_download_by_ids" name="Download IDR/OMERO" version="0.44.1" profile="18.09">
+<tool id="idr_download_by_ids" name="Download IDR/OMERO" version="0.45" profile="18.09">
     <description></description>
     <macros>
         <xml name="region_spec" token_pos="upper-left corner">
@@ -19,8 +19,8 @@
         <edam_operation>operation_3443</edam_operation>
     </edam_operations>
     <requirements>
-        <requirement type="package" version="5.10.1">omero-py</requirement>
-        <requirement type="package" version="0.4.2">pylibtiff</requirement>
+        <requirement type="package" version="5.19.4">omero-py</requirement>
+        <requirement type="package" version="0.6.1">pylibtiff</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         

From 41c6d004b855602256172b23303d7d21f24e0d77 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Wed, 25 Sep 2024 17:36:17 +0200
Subject: [PATCH 02/15] enable download of the full image (hyperstack)

---
 tools/idr_download/idr_download_by_ids.py  | 148 ++++++++++++++-------
 tools/idr_download/idr_download_by_ids.xml | 101 ++++++++++----
 2 files changed, 177 insertions(+), 72 deletions(-)

diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py
index 6c2adddf345..a399cc699af 100644
--- a/tools/idr_download/idr_download_by_ids.py
+++ b/tools/idr_download/idr_download_by_ids.py
@@ -5,7 +5,10 @@
 import tarfile
 from contextlib import ExitStack
 from tempfile import TemporaryDirectory
+from itertools import product
+import numpy
 
+from tifffile import imwrite
 from libtiff import TIFF
 from omero.cli import cli_login
 from omero.gateway import BlitzGateway  # noqa
@@ -110,9 +113,27 @@ def get_image_array(image, tile, z, c, t):
     return selection
 
 
+def get_full_image_array(image):
+    # The goal is to get the image in TZCYX order
+    pixels = image.getPrimaryPixels()
+    tzclist = list(product(range(image.getSizeT()), range(image.getSizeZ()), range(image.getSizeC())))
+    zctlist = [(z, c, t) for (t, z, c) in tzclist]
+    try:
+        all_planes = numpy.array(list(pixels.getPlanes(zctlist)))
+        all_planes_reshaped = all_planes.reshape(image.getSizeT(), image.getSizeZ(), image.getSizeC(), all_planes.shape[-2], all_planes.shape[-1])
+    except Exception as e:
+        warning = '{0} (ID: {1})'.format(image.getName(),
+                                         image.getId())
+        warn('Could not download the requested region', warning)
+        warn(e.msg)
+        return
+
+    return all_planes_reshaped
+
+
 def download_image_data(
     image_ids_or_dataset_id, dataset=False,
-    download_original=False,
+    download_original=False, download_full=False,
     channel=None, z_stack=0, frame=0,
     coord=(0, 0), width=0, height=0, region_spec='rectangle',
     skip_failed=False, download_tar=False, omero_host='idr.openmicroscopy.org', omero_secured=False, config_file=None
@@ -131,7 +152,7 @@ def download_image_data(
                 omero_username = 'public'
                 omero_password = 'public'
 
-    if not download_original and region_spec not in ['rectangle', 'center']:
+    if not download_original and not download_full and region_spec not in ['rectangle', 'center']:
         raise ValueError(
             'Got unknown value "{0}" as region_spec argument'
             .format(region_spec)
@@ -226,16 +247,79 @@ def download_image_data(
                     'database. Aborting!'
                     .format(image_warning_id)
                 )
-            if not download_original:
+            try:
+                # try to extract image name
+                # if anything goes wrong here skip the image
+                # or abort.
+                image_name = os.path.splitext(image.getName())[0]
+                image_warning_id = '{0} (ID: {1})'.format(
+                    image_name, image_id
+                )
+            except Exception as e:
+                # respect skip_failed on unexpected errors
+                if skip_failed:
+                    warn(str(e), image_warning_id, warn_skip=True)
+                    continue
+                else:
+                    raise
+            if download_full:
+                fname = '__'.join([image_name.replace(' ', '_'), str(image_id), "full"]) + '.tiff'
+                # download and save the region as TIFF
+                try:
+                    im_array = get_full_image_array(image)
+
+                    if download_tar:
+                        fname = os.path.join(tempdir, fname)
+
+                    imwrite(fname, im_array, imagej=True)
+                    # move image into tarball
+                    if download_tar:
+                        archive.add(fname, os.path.basename(fname))
+                        os.remove(fname)
+                except Exception as e:
+                    if skip_failed:
+                        # respect skip_failed on unexpected errors
+                        warn(str(e), image_warning_id, warn_skip=True)
+                        continue
+                    else:
+                        raise
+
+            elif download_original:
+                try:
+                    # try to extract image properties
+                    # if anything goes wrong here skip the image
+                    # or abort.
+                    original_image_name = image.getFileset().listFiles()[0].getName()
+                    fname = image_name + "__" + str(image_id) + os.path.splitext(original_image_name)[1]
+                    fname = fname.replace(' ', '_')
+                    fname = fname.replace('/', '_')
+                    download_directory = "./"
+                    if download_tar:
+                        download_directory = tempdir
+                    with cli_login("-u", omero_username, "-s", omero_host, "-w", omero_password) as cli:
+                        cli.invoke(["download", f"Image:{image_id}", download_directory])
+                        if cli.rv != 0:
+                            raise Exception("Download failed.")
+                    # This will download to download_directory/original_image_name
+                    os.rename(os.path.join(download_directory, original_image_name),
+                              os.path.join(download_directory, fname))
+                    # move image into tarball
+                    if download_tar:
+                        archive.add(os.path.join(download_directory, fname),
+                                    os.path.basename(fname))
+                        os.remove(os.path.join(download_directory, fname))
+                except Exception as e:
+                    # respect skip_failed on unexpected errors
+                    if skip_failed:
+                        warn(str(e), image_warning_id, warn_skip=True)
+                        continue
+                    else:
+                        raise
+            else:
                 try:
                     # try to extract image properties
                     # if anything goes wrong here skip the image
                     # or abort.
-                    image_name = os.path.splitext(image.getName())[0]
-                    image_warning_id = '{0} (ID: {1})'.format(
-                        image_name, image_id
-                    )
-
                     if region_spec == 'rectangle':
                         tile = get_clipping_region(image, *coord, width, height)
                     elif region_spec == 'center':
@@ -314,16 +398,13 @@ def download_image_data(
                                 .format(channel, image_warning_id)
                             )
 
-                # download and save the region as TIFF
                 fname = '__'.join(
                     [image_name, str(image_id)] + [str(x) for x in tile]
                 )
+                fname += '.tiff'
+                fname = fname.replace(' ', '_')
+                # download and save the region as TIFF
                 try:
-                    if fname[-5:] != '.tiff':
-                        fname += '.tiff'
-
-                    fname = fname.replace(' ', '_')
-
                     im_array = get_image_array(image, tile, z_stack, channel_index, frame)
 
                     if download_tar:
@@ -344,41 +425,6 @@ def download_image_data(
                         continue
                     else:
                         raise
-            else:
-                try:
-                    # try to extract image properties
-                    # if anything goes wrong here skip the image
-                    # or abort.
-                    image_name = os.path.splitext(image.getName())[0]
-                    image_warning_id = '{0} (ID: {1})'.format(
-                        image_name, image_id
-                    )
-                    original_image_name = image.getFileset().listFiles()[0].getName()
-                    fname = image_name + "__" + str(image_id) + os.path.splitext(original_image_name)[1]
-                    fname = fname.replace(' ', '_')
-                    fname = fname.replace('/', '_')
-                    download_directory = "./"
-                    if download_tar:
-                        download_directory = tempdir
-                    with cli_login("-u", omero_username, "-s", omero_host, "-w", omero_password) as cli:
-                        cli.invoke(["download", f"Image:{image_id}", download_directory])
-                        if cli.rv != 0:
-                            raise Exception("Download failed.")
-                    # This will download to download_directory/original_image_name
-                    os.rename(os.path.join(download_directory, original_image_name),
-                              os.path.join(download_directory, fname))
-                    # move image into tarball
-                    if download_tar:
-                        archive.add(os.path.join(download_directory, fname),
-                                    os.path.basename(fname))
-                        os.remove(os.path.join(download_directory, fname))
-                except Exception as e:
-                    # respect skip_failed on unexpected errors
-                    if skip_failed:
-                        warn(str(e), image_warning_id, warn_skip=True)
-                        continue
-                    else:
-                        raise
 
 
 def _center_to_ul(center_x, center_y, width, height):
@@ -409,6 +455,10 @@ def _center_to_ul(center_x, center_y, width, height):
         '--download-original', dest='download_original', action='store_true',
         help="download the original file uploaded to omero"
     )
+    p.add_argument(
+        '--download-full', dest='download_full', action='store_true',
+        help="download the full image on omero"
+    )
     p.add_argument(
         '-c', '--channel',
         help='name of the channel to retrieve data for '
diff --git a/tools/idr_download/idr_download_by_ids.xml b/tools/idr_download/idr_download_by_ids.xml
index 5e3395043dc..f42af81814b 100644
--- a/tools/idr_download/idr_download_by_ids.xml
+++ b/tools/idr_download/idr_download_by_ids.xml
@@ -21,6 +21,7 @@
     <requirements>
         <requirement type="package" version="5.19.4">omero-py</requirement>
         <requirement type="package" version="0.6.1">pylibtiff</requirement>
+        <requirement type="package" version="2024.9.20">tifffile</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         
@@ -51,6 +52,8 @@
         #end if
         #if $image_region.original == "original":
             --download-original
+        #elif $image_region.original == "full":
+            --download-full
         #else:
             #set $channel = str($image_region.channel).strip()
             #if $channel:
@@ -87,7 +90,7 @@
 }
         ]]></configfile>
     </configfiles>
-<inputs>
+    <inputs>
         <conditional name="omero_instance_type">
             <param name="omero_instance" type="select" label="Which OMERO instance to connect?"
                    help="By default, the tool will download a tarball containing individual images from IDR into your Galaxy history. If you 
@@ -135,9 +138,11 @@
         <conditional name="image_region">
             <param name="original" type="select" label="Which images do you want to download?">
                 <option value="TIFF" selected="true">Exported TIFF (single channel, single stack)</option>
+                <option value="full" >Whole TIFF (all channels, all frames, all stacks)</option>
                 <option value="original">Original file (file uploaded to omero, only available for private instances)</option>
             </param>
             <when value="original"/>
+            <when value="full"/>
             <when value="TIFF">
                 <param name="channel" type="text"
                     label="Name of the channel to download"
@@ -182,7 +187,7 @@
         </data> 
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <conditional name="omero_instance_type">
                  <param name="omero_instance" value="idr" />
             </conditional>
@@ -202,10 +207,10 @@
             </conditional>
             <param name="download_tar" value="false" />
             <output_collection name="output_file" type="list">
-                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test0.tiff"/>
+                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test0.tiff" compare="image_diff" />
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <conditional name="omero_instance_type">
                  <param name="omero_instance" value="idr" />
             </conditional>
@@ -225,10 +230,10 @@
             </conditional>
             <param name="download_tar" value="false" />
             <output_collection name="output_file" type="list">
-                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test1.tiff"/>
+                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test1.tiff" compare="image_diff"/>
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <conditional name="omero_instance_type">
                  <param name="omero_instance" value="idr" />
             </conditional>
@@ -248,10 +253,10 @@
             </conditional>
             <param name="download_tar" value="false" />
             <output_collection name="output_file" type="list">
-                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test2.tiff"/>
+                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test2.tiff" compare="image_diff"/>
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <conditional name="omero_instance_type">
                  <param name="omero_instance" value="idr" />
             </conditional>
@@ -270,7 +275,11 @@
             <output_collection name="output_file" type="list" count="3">
                 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024">
                     <assert_contents>
-                        <has_size value="2097286" />
+                        <has_size size="2097286" />
+                        <has_image_width width="1024" />
+                        <has_image_height height="1024" />
+                        <has_image_mean_intensity mean_intensity="320.868" />
+                        <has_image_center_of_mass center_of_mass="541.664, 456.743" />
                     </assert_contents>
                 </element>
             </output_collection>
@@ -299,7 +308,7 @@
             </conditional>
             <param name="download_tar" value="false" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <!-- Repeat test with non-existing image-ID 9036708999,
             but use skip-failed option -->
             <conditional name="omero_instance_type">
@@ -321,7 +330,11 @@
             <output_collection name="output_file" type="list" count="2">
                 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024">
                     <assert_contents>
-                        <has_size value="2097286" />
+                        <has_size size="2097286" />
+                        <has_image_width width="1024" />
+                        <has_image_height height="1024" />
+                        <has_image_mean_intensity mean_intensity="320.868" />
+                        <has_image_center_of_mass center_of_mass="541.664, 456.743" />
                     </assert_contents>
                 </element>
             </output_collection>
@@ -333,7 +346,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <conditional name="omero_instance_type">
                  <param name="omero_instance" value="idr" />
             </conditional>
@@ -354,17 +367,25 @@
             </conditional>
             <output name="output_tar">
                     <assert_contents>
-                        <has_size value="1382400" />
+                        <has_size size="1382400" />
                         <has_archive_member path=".*/*__1828167__0__0__671__511.tiff" >
-                            <has_size value="685896" />
+                            <has_size size="685896" />
+                            <has_image_width width="671" />
+                            <has_image_height height="511" />
+                            <has_image_mean_intensity mean_intensity="388.711" />
+                            <has_image_center_of_mass center_of_mass="354.627, 267" />
                         </has_archive_member>
                         <has_archive_member path=".*/*__1828658__0__0__671__511.tiff" >
-                            <has_size value="685896" />
+                            <has_size size="685896" />
+                            <has_image_width width="671" />
+                            <has_image_height height="511" />
+                            <has_image_mean_intensity mean_intensity="397.507" />
+                            <has_image_center_of_mass center_of_mass="346.098, 250.652" />
                         </has_archive_member>
                     </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <conditional name="omero_instance_type">
                  <param name="omero_instance" value="priv" />
                  <param name="omero_host" value="idr.openmicroscopy.org" />
@@ -387,7 +408,7 @@
             </conditional>
             <param name="download_tar" value="false" />
             <output_collection name="output_file" type="list">
-                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" file="test0.tiff"/>
+                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" file="test0.tiff" compare="image_diff"/>
             </output_collection>
         </test>
         <test expect_failure="true">
@@ -415,7 +436,7 @@
                 <has_text text="OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" />
             </assert_stderr >
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <conditional name="omero_instance_type">
                  <param name="omero_instance" value="idr" />
             </conditional>
@@ -426,27 +447,43 @@
             <output_collection name="output_file" type="list" count="4">
                 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024">
                     <assert_contents>
-                        <has_size value="2097286" />
+                        <has_size size="2097286" />
+                        <has_image_width width="1024" />
+                        <has_image_height height="1024" />
+                        <has_image_mean_intensity mean_intensity="145.310" />
+                        <has_image_center_of_mass center_of_mass="527.499, 480.704" />
                     </assert_contents>
                 </element>
                 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_D3D__9036708__0__0__1024__1024">
                     <assert_contents>
-                        <has_size value="2097286" />
+                        <has_size size="2097286" />
+                        <has_image_width width="1024" />
+                        <has_image_height height="1024" />
+                        <has_image_mean_intensity mean_intensity="147.025" />
+                        <has_image_center_of_mass center_of_mass="528.977, 480.691" />
                     </assert_contents>
                 </element>
                 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_D3D_zproj__9036710__0__0__1024__1024">
                     <assert_contents>
-                        <has_size value="2097286" />
+                        <has_size size="2097286" />
+                        <has_image_width width="1024" />
+                        <has_image_height height="1024" />
+                        <has_image_mean_intensity mean_intensity="210.787" />
+                        <has_image_center_of_mass center_of_mass="534.629, 473.267" />
                     </assert_contents>
                 </element>
                 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_REF__9036709__0__0__1024__1024">
                     <assert_contents>
-                        <has_size value="2097286" />
+                        <has_size size="2097286" />
+                        <has_image_width width="1024" />
+                        <has_image_height height="1024" />
+                        <has_image_mean_intensity mean_intensity="3816.051" />
+                        <has_image_center_of_mass center_of_mass="512.274, 503.186" />
                     </assert_contents>
                 </element>
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <conditional name="omero_instance_type">
                  <param name="omero_instance" value="idr" />
             </conditional>
@@ -462,6 +499,24 @@
             <output_collection name="output_file" type="list" count="0">
             </output_collection>
         </test>
+        <test expect_num_outputs="2">
+            <conditional name="omero_instance_type">
+                 <param name="omero_instance" value="idr" />
+            </conditional>
+            <param name="source" value="link" />
+            <param name="id_spec" value="1229801" />
+            <param name="download_tar" value="false" />
+            <conditional name="image_region">
+                <param name="original" value="full"/> 
+            </conditional>
+            <output_collection name="output_file" type="list" count="1">
+                <element name="JL_120731_S6A_[Well_A-1;_Field_#1]__1229801__full">
+                    <assert_contents>
+                        <has_size size="91592058" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
     </tests>
     <help><![CDATA[
 Download image data from the IDR_ (Image Data Resource) - a public repository

From ec4ea7c283bd3f3907d239e71bd56438b6312421 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Wed, 25 Sep 2024 17:36:47 +0200
Subject: [PATCH 03/15] run isort

---
 tools/idr_download/idr_download_by_ids.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py
index a399cc699af..f630b1feb29 100644
--- a/tools/idr_download/idr_download_by_ids.py
+++ b/tools/idr_download/idr_download_by_ids.py
@@ -4,15 +4,15 @@
 import sys
 import tarfile
 from contextlib import ExitStack
-from tempfile import TemporaryDirectory
 from itertools import product
-import numpy
+from tempfile import TemporaryDirectory
 
-from tifffile import imwrite
+import numpy
 from libtiff import TIFF
 from omero.cli import cli_login
-from omero.gateway import BlitzGateway  # noqa
 from omero.constants.namespaces import NSBULKANNOTATIONS  # noqa
+from omero.gateway import BlitzGateway  # noqa
+from tifffile import imwrite
 
 
 def warn(message, image_identifier, warn_skip=False):

From 62767452d5453019198cdf1d466765fbe3411d20 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Wed, 25 Sep 2024 17:36:59 +0200
Subject: [PATCH 04/15] run black

---
 tools/idr_download/idr_download_by_ids.py | 344 ++++++++++++----------
 1 file changed, 181 insertions(+), 163 deletions(-)

diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py
index f630b1feb29..62e599f9373 100644
--- a/tools/idr_download/idr_download_by_ids.py
+++ b/tools/idr_download/idr_download_by_ids.py
@@ -18,20 +18,15 @@
 def warn(message, image_identifier, warn_skip=False):
     message = message.rstrip()
     if warn_skip:
-        if message[-1] in ['.', '!', '?']:
-            skip_msg = ' Skipping download!'
+        if message[-1] in [".", "!", "?"]:
+            skip_msg = " Skipping download!"
         else:
-            skip_msg = '. Skipping download!'
+            skip_msg = ". Skipping download!"
     else:
-        skip_msg = ''
+        skip_msg = ""
     print(
-        'ImageSpecWarning for {0}: {1}{2}'
-        .format(
-            image_identifier,
-            message,
-            skip_msg
-        ),
-        file=sys.stderr
+        "ImageSpecWarning for {0}: {1}{2}".format(image_identifier, message, skip_msg),
+        file=sys.stderr,
     )
 
 
@@ -47,7 +42,7 @@ def find_channel_index(image, channel_name):
             if p[0] == "Channels":
                 channels = p[1].replace(" ", "").split(";")
                 for n, c in enumerate(channels):
-                    for value in c.split(':'):
+                    for value in c.split(":"):
                         if channel_name == value.lower():
                             return n
     return -1
@@ -61,16 +56,16 @@ def get_clipping_region(image, x, y, w, h):
     # It may be better to abort in this situation.
     if x < 0 or y < 0:
         raise ValueError(
-            'Too small upper left coordinate ({0}, {1}) for clipping region.'
-            .format(x, y)
+            "Too small upper left coordinate ({0}, {1}) for clipping region.".format(
+                x, y
+            )
         )
     size_x = image.getSizeX()
     size_y = image.getSizeY()
     if x >= size_x or y >= size_y:
         raise ValueError(
-            'Upper left coordinate ({0}, {1}) of clipping region lies '
-            'outside of image.'
-            .format(x, y)
+            "Upper left coordinate ({0}, {1}) of clipping region lies "
+            "outside of image.".format(x, y)
         )
     # adjust width and height to the image dimensions
     if w <= 0 or x + w > size_x:
@@ -105,9 +100,8 @@ def get_image_array(image, tile, z, c, t):
     try:
         selection = pixels.getTile(theZ=z, theT=t, theC=c, tile=tile)
     except Exception:
-        warning = '{0} (ID: {1})'.format(image.getName(),
-                                         image.getId())
-        warn('Could not download the requested region', warning)
+        warning = "{0} (ID: {1})".format(image.getName(), image.getId())
+        warn("Could not download the requested region", warning)
         return
 
     return selection
@@ -116,15 +110,24 @@ def get_image_array(image, tile, z, c, t):
 def get_full_image_array(image):
     # The goal is to get the image in TZCYX order
     pixels = image.getPrimaryPixels()
-    tzclist = list(product(range(image.getSizeT()), range(image.getSizeZ()), range(image.getSizeC())))
+    tzclist = list(
+        product(
+            range(image.getSizeT()), range(image.getSizeZ()), range(image.getSizeC())
+        )
+    )
     zctlist = [(z, c, t) for (t, z, c) in tzclist]
     try:
         all_planes = numpy.array(list(pixels.getPlanes(zctlist)))
-        all_planes_reshaped = all_planes.reshape(image.getSizeT(), image.getSizeZ(), image.getSizeC(), all_planes.shape[-2], all_planes.shape[-1])
+        all_planes_reshaped = all_planes.reshape(
+            image.getSizeT(),
+            image.getSizeZ(),
+            image.getSizeC(),
+            all_planes.shape[-2],
+            all_planes.shape[-1],
+        )
     except Exception as e:
-        warning = '{0} (ID: {1})'.format(image.getName(),
-                                         image.getId())
-        warn('Could not download the requested region', warning)
+        warning = "{0} (ID: {1})".format(image.getName(), image.getId())
+        warn("Could not download the requested region", warning)
         warn(e.msg)
         return
 
@@ -132,51 +135,59 @@ def get_full_image_array(image):
 
 
 def download_image_data(
-    image_ids_or_dataset_id, dataset=False,
-    download_original=False, download_full=False,
-    channel=None, z_stack=0, frame=0,
-    coord=(0, 0), width=0, height=0, region_spec='rectangle',
-    skip_failed=False, download_tar=False, omero_host='idr.openmicroscopy.org', omero_secured=False, config_file=None
+    image_ids_or_dataset_id,
+    dataset=False,
+    download_original=False,
+    download_full=False,
+    channel=None,
+    z_stack=0,
+    frame=0,
+    coord=(0, 0),
+    width=0,
+    height=0,
+    region_spec="rectangle",
+    skip_failed=False,
+    download_tar=False,
+    omero_host="idr.openmicroscopy.org",
+    omero_secured=False,
+    config_file=None,
 ):
 
     if config_file is None:  # IDR connection
-        omero_username = 'public'
-        omero_password = 'public'
+        omero_username = "public"
+        omero_password = "public"
     else:  # other omero instance
         with open(config_file) as f:
             cfg = json.load(f)
-            omero_username = cfg['username']
-            omero_password = cfg['password']
+            omero_username = cfg["username"]
+            omero_password = cfg["password"]
 
             if omero_username == "" or omero_password == "":
-                omero_username = 'public'
-                omero_password = 'public'
-
-    if not download_original and not download_full and region_spec not in ['rectangle', 'center']:
+                omero_username = "public"
+                omero_password = "public"
+
+    if (
+        not download_original
+        and not download_full
+        and region_spec not in ["rectangle", "center"]
+    ):
         raise ValueError(
-            'Got unknown value "{0}" as region_spec argument'
-            .format(region_spec)
+            'Got unknown value "{0}" as region_spec argument'.format(region_spec)
         )
     with ExitStack() as exit_stack:
         conn = exit_stack.enter_context(
             BlitzGateway(
-                omero_username, omero_password,
-                host=omero_host,
-                secure=omero_secured
+                omero_username, omero_password, host=omero_host, secure=omero_secured
             )
         )
         # exit_stack.callback(conn.connect().close)
         if download_tar:
             # create an archive file to write images to
-            archive = exit_stack.enter_context(
-                tarfile.open('images.tar', mode='w')
-            )
-            tempdir = exit_stack.enter_context(
-                TemporaryDirectory()
-            )
+            archive = exit_stack.enter_context(tarfile.open("images.tar", mode="w"))
+            tempdir = exit_stack.enter_context(TemporaryDirectory())
 
         if dataset:
-            dataset_warning_id = 'Dataset-ID: {0}'.format(image_ids_or_dataset_id[0])
+            dataset_warning_id = "Dataset-ID: {0}".format(image_ids_or_dataset_id[0])
             try:
                 dataset_id = int(image_ids_or_dataset_id[0])
             except ValueError:
@@ -196,28 +207,26 @@ def download_image_data(
             if image_ids is None:
                 if skip_failed:
                     warn(
-                        'Unable to find a dataset with this ID in the '
-                        'database.',
+                        "Unable to find a dataset with this ID in the " "database.",
                         dataset_warning_id,
-                        warn_skip=True
+                        warn_skip=True,
                     )
                 else:
                     raise ValueError(
-                        '{0}: Unable to find a dataset with this ID in the '
-                        'database. Aborting!'
-                        .format(dataset_warning_id)
+                        "{0}: Unable to find a dataset with this ID in the "
+                        "database. Aborting!".format(dataset_warning_id)
                     )
 
         else:
             # basic argument sanity checks and adjustments
-            prefix = 'image-'
+            prefix = "image-"
             # normalize image ids by stripping off prefix if it exists
             image_ids = [
-                iid[len(prefix):] if iid[:len(prefix)] == prefix else iid
+                iid[len(prefix) :] if iid[: len(prefix)] == prefix else iid
                 for iid in image_ids_or_dataset_id
             ]
         for image_id in image_ids:
-            image_warning_id = 'Image-ID: {0}'.format(image_id)
+            image_warning_id = "Image-ID: {0}".format(image_id)
             try:
                 image_id = int(image_id)
             except ValueError:
@@ -236,25 +245,21 @@ def download_image_data(
             if image is None:
                 if skip_failed:
                     warn(
-                        'Unable to find an image with this ID in the '
-                        'database.',
+                        "Unable to find an image with this ID in the " "database.",
                         image_warning_id,
-                        warn_skip=True
+                        warn_skip=True,
                     )
                     continue
                 raise ValueError(
-                    '{0}: Unable to find an image with this ID in the '
-                    'database. Aborting!'
-                    .format(image_warning_id)
+                    "{0}: Unable to find an image with this ID in the "
+                    "database. Aborting!".format(image_warning_id)
                 )
             try:
                 # try to extract image name
                 # if anything goes wrong here skip the image
                 # or abort.
                 image_name = os.path.splitext(image.getName())[0]
-                image_warning_id = '{0} (ID: {1})'.format(
-                    image_name, image_id
-                )
+                image_warning_id = "{0} (ID: {1})".format(image_name, image_id)
             except Exception as e:
                 # respect skip_failed on unexpected errors
                 if skip_failed:
@@ -263,7 +268,10 @@ def download_image_data(
                 else:
                     raise
             if download_full:
-                fname = '__'.join([image_name.replace(' ', '_'), str(image_id), "full"]) + '.tiff'
+                fname = (
+                    "__".join([image_name.replace(" ", "_"), str(image_id), "full"])
+                    + ".tiff"
+                )
                 # download and save the region as TIFF
                 try:
                     im_array = get_full_image_array(image)
@@ -290,23 +298,36 @@ def download_image_data(
                     # if anything goes wrong here skip the image
                     # or abort.
                     original_image_name = image.getFileset().listFiles()[0].getName()
-                    fname = image_name + "__" + str(image_id) + os.path.splitext(original_image_name)[1]
-                    fname = fname.replace(' ', '_')
-                    fname = fname.replace('/', '_')
+                    fname = (
+                        image_name
+                        + "__"
+                        + str(image_id)
+                        + os.path.splitext(original_image_name)[1]
+                    )
+                    fname = fname.replace(" ", "_")
+                    fname = fname.replace("/", "_")
                     download_directory = "./"
                     if download_tar:
                         download_directory = tempdir
-                    with cli_login("-u", omero_username, "-s", omero_host, "-w", omero_password) as cli:
-                        cli.invoke(["download", f"Image:{image_id}", download_directory])
+                    with cli_login(
+                        "-u", omero_username, "-s", omero_host, "-w", omero_password
+                    ) as cli:
+                        cli.invoke(
+                            ["download", f"Image:{image_id}", download_directory]
+                        )
                         if cli.rv != 0:
                             raise Exception("Download failed.")
                     # This will download to download_directory/original_image_name
-                    os.rename(os.path.join(download_directory, original_image_name),
-                              os.path.join(download_directory, fname))
+                    os.rename(
+                        os.path.join(download_directory, original_image_name),
+                        os.path.join(download_directory, fname),
+                    )
                     # move image into tarball
                     if download_tar:
-                        archive.add(os.path.join(download_directory, fname),
-                                    os.path.basename(fname))
+                        archive.add(
+                            os.path.join(download_directory, fname),
+                            os.path.basename(fname),
+                        )
                         os.remove(os.path.join(download_directory, fname))
                 except Exception as e:
                     # respect skip_failed on unexpected errors
@@ -320,12 +341,11 @@ def download_image_data(
                     # try to extract image properties
                     # if anything goes wrong here skip the image
                     # or abort.
-                    if region_spec == 'rectangle':
+                    if region_spec == "rectangle":
                         tile = get_clipping_region(image, *coord, width, height)
-                    elif region_spec == 'center':
+                    elif region_spec == "center":
                         tile = get_clipping_region(
-                            image,
-                            *_center_to_ul(*coord, width, height)
+                            image, *_center_to_ul(*coord, width, height)
                         )
 
                     ori_z, z_stack = z_stack, confine_plane(image, z_stack)
@@ -348,69 +368,66 @@ def download_image_data(
                     # The downloaded image region will have smaller dimensions
                     # than the specified width x height.
                     warn(
-                        'Downloaded image dimensions ({0} x {1}) will be smaller '
-                        'than the specified width and height ({2} x {3}).'
-                        .format(tile[2], tile[3], width, height),
-                        image_warning_id
+                        "Downloaded image dimensions ({0} x {1}) will be smaller "
+                        "than the specified width and height ({2} x {3}).".format(
+                            tile[2], tile[3], width, height
+                        ),
+                        image_warning_id,
                     )
 
                 # z-stack sanity checks and warnings
                 if z_stack != ori_z:
                     warn(
-                        'Specified image plane ({0}) is out of bounds. Using {1} '
-                        'instead.'
-                        .format(ori_z, z_stack),
-                        image_warning_id
+                        "Specified image plane ({0}) is out of bounds. Using {1} "
+                        "instead.".format(ori_z, z_stack),
+                        image_warning_id,
                     )
 
                 # frame sanity checks and warnings
                 if frame != ori_frame:
                     warn(
-                        'Specified image frame ({0}) is out of bounds. Using '
-                        'frame {1} instead.'
-                        .format(ori_frame, frame),
-                        image_warning_id
+                        "Specified image frame ({0}) is out of bounds. Using "
+                        "frame {1} instead.".format(ori_frame, frame),
+                        image_warning_id,
                     )
 
                 # channel index sanity checks and warnings
                 if channel is None:
                     if num_channels > 1:
                         warn(
-                            'No specific channel selected for multi-channel '
-                            'image. Using first of {0} channels.'
-                            .format(num_channels),
-                            image_warning_id
+                            "No specific channel selected for multi-channel "
+                            "image. Using first of {0} channels.".format(num_channels),
+                            image_warning_id,
                         )
                 else:
                     if channel_index == -1 or channel_index >= num_channels:
                         if skip_failed:
                             warn(
                                 str(channel)
-                                + ' is not a known channel name for this image.',
+                                + " is not a known channel name for this image.",
                                 image_warning_id,
-                                warn_skip=True
+                                warn_skip=True,
                             )
                             continue
                         else:
                             raise ValueError(
                                 '"{0}" is not a known channel name for image {1}. '
-                                'Aborting!'
-                                .format(channel, image_warning_id)
+                                "Aborting!".format(channel, image_warning_id)
                             )
 
-                fname = '__'.join(
-                    [image_name, str(image_id)] + [str(x) for x in tile]
-                )
-                fname += '.tiff'
-                fname = fname.replace(' ', '_')
+                fname = "__".join([image_name, str(image_id)] + [str(x) for x in tile])
+                fname += ".tiff"
+                fname = fname.replace(" ", "_")
                 # download and save the region as TIFF
                 try:
-                    im_array = get_image_array(image, tile, z_stack, channel_index, frame)
+                    im_array = get_image_array(
+                        image, tile, z_stack, channel_index, frame
+                    )
 
                     if download_tar:
                         fname = os.path.join(tempdir, fname)
                     try:
-                        tiff = TIFF.open(fname, mode='w')
+                        tiff = TIFF.open(fname, mode="w")
                         tiff.write_image(im_array)
                     finally:
                         tiff.close()
@@ -446,81 +463,82 @@ def _center_to_ul(center_x, center_y, width, height):
 if __name__ == "__main__":
     p = argparse.ArgumentParser()
     p.add_argument(
-        'image_ids_or_dataset_id', nargs='*', default=[],
-        help='one or more IDR image ids or a single dataset id'
-             'for which to retrieve data (default: '
-             'read ids from stdin).'
+        "image_ids_or_dataset_id",
+        nargs="*",
+        default=[],
+        help="one or more IDR image ids or a single dataset id"
+        "for which to retrieve data (default: "
+        "read ids from stdin).",
     )
     p.add_argument(
-        '--download-original', dest='download_original', action='store_true',
-        help="download the original file uploaded to omero"
+        "--download-original",
+        dest="download_original",
+        action="store_true",
+        help="download the original file uploaded to omero",
     )
     p.add_argument(
-        '--download-full', dest='download_full', action='store_true',
-        help="download the full image on omero"
+        "--download-full",
+        dest="download_full",
+        action="store_true",
+        help="download the full image on omero",
     )
     p.add_argument(
-        '-c', '--channel',
-        help='name of the channel to retrieve data for '
-             '(note: the first channel of each image will be downloaded if '
-             'left unspecified)'
+        "-c",
+        "--channel",
+        help="name of the channel to retrieve data for "
+        "(note: the first channel of each image will be downloaded if "
+        "left unspecified)",
     )
     region = p.add_mutually_exclusive_group()
     region.add_argument(
-        '--rectangle', nargs=4, type=int, default=argparse.SUPPRESS,
-        help='specify a clipping region for the image as x y width height, '
-             'where x and y give the upper left coordinate of the rectangle '
-             'to clip to. Set width and height to 0 to extend the rectangle '
-             'to the actual size of the image.'
+        "--rectangle",
+        nargs=4,
+        type=int,
+        default=argparse.SUPPRESS,
+        help="specify a clipping region for the image as x y width height, "
+        "where x and y give the upper left coordinate of the rectangle "
+        "to clip to. Set width and height to 0 to extend the rectangle "
+        "to the actual size of the image.",
     )
     region.add_argument(
-        '--center', nargs=4, type=int, default=argparse.SUPPRESS,
-        help='specify a clipping region for the image as x y width height, '
-             'where x and y define the center of a width x height rectangle. '
-             'Set either width or height to 0 to extend the region to the '
-             'actual size of the image along the x- or y-axis.\n'
-             'Note: Even values for width and height will be rounded down to '
-             'the nearest odd number.'
-    )
-    p.add_argument(
-        '-f', '--frame', type=int, default=0
-    )
-    p.add_argument(
-        '-z', '--z-stack', type=int, default=0
-    )
-    p.add_argument(
-        '--skip-failed', action='store_true'
-    )
-    p.add_argument(
-        '--download-tar', action='store_true'
-    )
-    p.add_argument(
-        '-oh', '--omero-host', type=str, default="idr.openmicroscopy.org"
-    )
-    p.add_argument(
-        '--omero-secured', action='store_true', default=True
-    )
-    p.add_argument(
-        '-cf', '--config-file', dest='config_file', default=None
-    )
-    p.add_argument(
-        '--dataset', action='store_true'
+        "--center",
+        nargs=4,
+        type=int,
+        default=argparse.SUPPRESS,
+        help="specify a clipping region for the image as x y width height, "
+        "where x and y define the center of a width x height rectangle. "
+        "Set either width or height to 0 to extend the region to the "
+        "actual size of the image along the x- or y-axis.\n"
+        "Note: Even values for width and height will be rounded down to "
+        "the nearest odd number.",
     )
+    p.add_argument("-f", "--frame", type=int, default=0)
+    p.add_argument("-z", "--z-stack", type=int, default=0)
+    p.add_argument("--skip-failed", action="store_true")
+    p.add_argument("--download-tar", action="store_true")
+    p.add_argument("-oh", "--omero-host", type=str, default="idr.openmicroscopy.org")
+    p.add_argument("--omero-secured", action="store_true", default=True)
+    p.add_argument("-cf", "--config-file", dest="config_file", default=None)
+    p.add_argument("--dataset", action="store_true")
     args = p.parse_args()
     if not args.image_ids_or_dataset_id:
         args.image_ids_or_dataset_id = sys.stdin.read().split()
     if args.dataset and len(args.image_ids_or_dataset_id) > 1:
         warn("Multiple dataset ids provided. Only the first one will be used.")
-    if 'center' in args:
+    if "center" in args:
         args.coord, args.width, args.height = (
-            args.center[:2], args.center[2], args.center[3]
+            args.center[:2],
+            args.center[2],
+            args.center[3],
         )
-        args.region_spec = 'center'
+        args.region_spec = "center"
         del args.center
-    elif 'rectangle' in args:
+    elif "rectangle" in args:
         args.coord, args.width, args.height = (
-            args.rectangle[:2], args.rectangle[2], args.rectangle[3]
+            args.rectangle[:2],
+            args.rectangle[2],
+            args.rectangle[3],
         )
-        args.region_spec = 'rectangle'
+        args.region_spec = "rectangle"
         del args.rectangle
     download_image_data(**vars(args))

From b7862310784a2088945d84a3df9942355e4beebc Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Wed, 25 Sep 2024 17:37:29 +0200
Subject: [PATCH 05/15] check flake8

---
 tools/idr_download/idr_download_by_ids.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py
index 62e599f9373..787e9faaab3 100644
--- a/tools/idr_download/idr_download_by_ids.py
+++ b/tools/idr_download/idr_download_by_ids.py
@@ -222,7 +222,7 @@ def download_image_data(
             prefix = "image-"
             # normalize image ids by stripping off prefix if it exists
             image_ids = [
-                iid[len(prefix) :] if iid[: len(prefix)] == prefix else iid
+                iid[len(prefix):] if iid[:len(prefix)] == prefix else iid
                 for iid in image_ids_or_dataset_id
             ]
         for image_id in image_ids:

From fe2d7396b32572f248d42606bb0caf44088befe3 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 26 Sep 2024 09:44:40 +0200
Subject: [PATCH 06/15] Apply suggestions from @kostrykin

Co-authored-by: Leonid Kostrykin <void@evoid.de>
---
 tools/idr_download/idr_download_by_ids.py  | 4 +---
 tools/idr_download/idr_download_by_ids.xml | 2 +-
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py
index 787e9faaab3..d1a60fed189 100644
--- a/tools/idr_download/idr_download_by_ids.py
+++ b/tools/idr_download/idr_download_by_ids.py
@@ -180,7 +180,6 @@ def download_image_data(
                 omero_username, omero_password, host=omero_host, secure=omero_secured
             )
         )
-        # exit_stack.callback(conn.connect().close)
         if download_tar:
             # create an archive file to write images to
             archive = exit_stack.enter_context(tarfile.open("images.tar", mode="w"))
@@ -245,7 +244,7 @@ def download_image_data(
             if image is None:
                 if skip_failed:
                     warn(
-                        "Unable to find an image with this ID in the " "database.",
+                        "Unable to find an image with this ID in the database.",
                         image_warning_id,
                         warn_skip=True,
                     )
@@ -291,7 +290,6 @@ def download_image_data(
                         continue
                     else:
                         raise
-
             elif download_original:
                 try:
                     # try to extract image properties
diff --git a/tools/idr_download/idr_download_by_ids.xml b/tools/idr_download/idr_download_by_ids.xml
index f42af81814b..a56d4f9684d 100644
--- a/tools/idr_download/idr_download_by_ids.xml
+++ b/tools/idr_download/idr_download_by_ids.xml
@@ -138,7 +138,7 @@
         <conditional name="image_region">
             <param name="original" type="select" label="Which images do you want to download?">
                 <option value="TIFF" selected="true">Exported TIFF (single channel, single stack)</option>
-                <option value="full" >Whole TIFF (all channels, all frames, all stacks)</option>
+                <option value="full">Whole TIFF (all channels, all frames, all stacks)</option>
                 <option value="original">Original file (file uploaded to omero, only available for private instances)</option>
             </param>
             <when value="original"/>

From b6f985894293b503ea4a2139f886ba79b20787c1 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 26 Sep 2024 09:46:23 +0200
Subject: [PATCH 07/15] remove noqa

---
 tools/idr_download/idr_download_by_ids.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py
index d1a60fed189..d4d0004b16a 100644
--- a/tools/idr_download/idr_download_by_ids.py
+++ b/tools/idr_download/idr_download_by_ids.py
@@ -10,8 +10,8 @@
 import numpy
 from libtiff import TIFF
 from omero.cli import cli_login
-from omero.constants.namespaces import NSBULKANNOTATIONS  # noqa
-from omero.gateway import BlitzGateway  # noqa
+from omero.constants.namespaces import NSBULKANNOTATIONS
+from omero.gateway import BlitzGateway
 from tifffile import imwrite
 
 

From ee4f66c602b458badbbd84e1fb11ea385f847da9 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 26 Sep 2024 10:22:52 +0200
Subject: [PATCH 08/15] add docstrings to all functions

---
 tools/idr_download/idr_download_by_ids.py | 119 ++++++++++++++++++++++
 1 file changed, 119 insertions(+)

diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py
index d4d0004b16a..84017a2f183 100644
--- a/tools/idr_download/idr_download_by_ids.py
+++ b/tools/idr_download/idr_download_by_ids.py
@@ -16,6 +16,15 @@
 
 
 def warn(message, image_identifier, warn_skip=False):
+    """Print an error message to stderr and
+    - prefix with the image identifier
+    - suffix with 'Skipping download!' if warn_skip is True
+
+    Args:
+        message (string): Message to print to stderr
+        image_identifier (string): Image identifier
+        warn_skip (bool, optional): Whether 'skipping download' should be suffix to the message. Defaults to False.
+    """
     message = message.rstrip()
     if warn_skip:
         if message[-1] in [".", "!", "?"]:
@@ -31,6 +40,15 @@ def warn(message, image_identifier, warn_skip=False):
 
 
 def find_channel_index(image, channel_name):
+    """Identify the channel index from the image and the channel name
+
+    Args:
+        image (omero.gateway._ImageWrapper): image wrapper on which the channel should be identified
+        channel_name (string): name of the channel to look for
+
+    Returns:
+        int: Index of the channel or -1 if was not found.
+    """
     channel_name = channel_name.lower()
     for n, channel in enumerate(image.getChannelLabels()):
         if channel_name == channel.lower():
@@ -49,6 +67,22 @@ def find_channel_index(image, channel_name):
 
 
 def get_clipping_region(image, x, y, w, h):
+    """Check x,y and adjust w,h to image size to be able to crop the image with these coordinates
+
+    Args:
+        image (omero.gateway._ImageWrapper): image wrapper on which region want to be cropped
+        x (int): left x coordinate
+        y (int): top y coordinate
+        w (int): width
+        h (int): height
+
+    Raises:
+        ValueError: if the x or y coordinates are negative.
+        ValueError: if the x or y coordinates are larger than the width or height of the image.
+
+    Returns:
+        list of int: new x, y, width, height adjusted to the image
+    """
     # If the (x, y) coordinate falls outside the image boundaries, we
     # cannot just shift it because that would render the meaning of
     # w and h undefined (should width and height be decreased or the whole
@@ -76,6 +110,15 @@ def get_clipping_region(image, x, y, w, h):
 
 
 def confine_plane(image, z):
+    """Adjust/Confine z to be among the possible z for the image
+
+    Args:
+        image (omero.gateway._ImageWrapper): image wrapper for which the z is adjusted
+        z (int): plane index that need to be confined
+
+    Returns:
+        int: confined z
+    """
     if z < 0:
         z = 0
     else:
@@ -86,6 +129,15 @@ def confine_plane(image, z):
 
 
 def confine_frame(image, t):
+    """Adjust/Confine t to be among the possible t for the image
+
+    Args:
+        image (omero.gateway._ImageWrapper): image wrapper for which the t is adjusted
+        t (int): frame index that need to be confined
+
+    Returns:
+        int: confined t
+    """
     if t < 0:
         t = 0
     else:
@@ -96,6 +148,18 @@ def confine_frame(image, t):
 
 
 def get_image_array(image, tile, z, c, t):
+    """Get a 2D numpy array from an image wrapper for a given tile, z, c, t
+
+    Args:
+        image (omero.gateway._ImageWrapper): image wrapper from which values are taken
+        tile (list of int): [x, y, width, height] where x,y is the top left coordinate of the region to crop
+        z (int): plane index
+        c (int): channel index
+        t (int): frame index
+
+    Returns:
+        numpy array of 2 dimensions: image values of the selected area
+    """
     pixels = image.getPrimaryPixels()
     try:
         selection = pixels.getTile(theZ=z, theT=t, theC=c, tile=tile)
@@ -108,13 +172,24 @@ def get_image_array(image, tile, z, c, t):
 
 
 def get_full_image_array(image):
+    """Get a 5D numpy array with all values from an image wrapper
+
+    Args:
+        image (omero.gateway._ImageWrapper): image wrapper from which values are taken
+
+    Returns:
+        numpy array of 5 dimensions: image values in the TZCYX order
+    """
     # The goal is to get the image in TZCYX order
     pixels = image.getPrimaryPixels()
+    # Get the final tzclist in the order that will make the numpy reshape work
     tzclist = list(
         product(
             range(image.getSizeT()), range(image.getSizeZ()), range(image.getSizeC())
         )
     )
+    # As getPlanes requires the indices in the zct order
+    # We keep the final order but switch indices
     zctlist = [(z, c, t) for (t, z, c) in tzclist]
     try:
         all_planes = numpy.array(list(pixels.getPlanes(zctlist)))
@@ -152,6 +227,39 @@ def download_image_data(
     omero_secured=False,
     config_file=None,
 ):
+    """Download the image data of
+      either a list of image ids or all images from a dataset.
+      The image data can be:
+       - a 2D cropped region or
+       - a hyperstack written in a tiff file
+       - the original image uploaded in omero
+      Optionally, th final file can be in a tar
+
+    Args:
+        image_ids_or_dataset_id (list of string): Can be either a list with a single id (int) of a dataset or a list with images ids (int) or images ids prefixed by 'image-'
+        dataset (bool, optional): Whether the image_ids_or_dataset_id is a dataset id and all images from this dataset should be retrieved (true) or image_ids_or_dataset_id are individual image ids (false). Defaults to False.
+        download_original (bool, optional): Whether the original file uploded to omero should be downloaded. Defaults to False.
+        download_full (bool, optional): Whether the full image (hyperstack) on omero should be written to TIFF. Defaults to False.
+        channel (string, optional): Channel name. Defaults to None.
+        z_stack (int, optional): Z stack (plane) index. Defaults to 0.
+        frame (int, optional): T frame index. Defaults to 0.
+        coord (tuple of int, optional): Coordinates of the top left or center of the region to crop. Defaults to (0, 0).
+        width (int, optional): Width of the region to crop. Defaults to 0.
+        height (int, optional): Height of the region to crop. Defaults to 0.
+        region_spec (str, optional): How the region is specified ('rectangle' = coord is top left or 'center' = the region is center). Defaults to "rectangle".
+        skip_failed (bool, optional): Do not stop the downloads if one fails. Defaults to False.
+        download_tar (bool, optional): Put all downloaded images into a tar file. Defaults to False.
+        omero_host (str, optional): omero host url. Defaults to "idr.openmicroscopy.org".
+        omero_secured (bool, optional): Whether the omero connects with secure connection. Defaults to False.
+        config_file (string, optional): File path with config file with credentials to connect to OMERO. Defaults to None.
+
+    Raises:
+        ValueError: If the region_spec is not 'rectangle' nor 'center' and a cropped region is wanted.
+        ValueError: If there is no dataset with this number in OMERO
+        ValueError: If there is no image with this number in OMERO
+        Exception: If the command to download the original image fails
+        ValueError: If the channel name could not be identified
+    """
 
     if config_file is None:  # IDR connection
         omero_username = "public"
@@ -443,6 +551,17 @@ def download_image_data(
 
 
 def _center_to_ul(center_x, center_y, width, height):
+    """Convert the center coordinates, width, height to upper left coordinates, width, height
+
+    Args:
+        center_x (int): x coordinate of center
+        center_y (int): y coordinate of center
+        width (int): width
+        height (int): height
+
+    Returns:
+        list of 4 int: x, y, width, height where x,y are the upper left coordinates
+    """
     if width > 0:
         ext_x = (width - 1) // 2
         ul_x = max([center_x - ext_x, 0])

From 0d9e4ec16d5f64ac6afae5a09f6b190fa74e05ae Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 26 Sep 2024 10:48:55 +0200
Subject: [PATCH 09/15] clarify the mutually exclusion of
 rectangle/center/download_full/download_original and the fact that
 channel/frame/z_stack are ignored if download_full or download_orignal is
 used.

---
 tools/idr_download/idr_download_by_ids.py | 73 ++++++++++++++---------
 1 file changed, 44 insertions(+), 29 deletions(-)

diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py
index 84017a2f183..bde548ac799 100644
--- a/tools/idr_download/idr_download_by_ids.py
+++ b/tools/idr_download/idr_download_by_ids.py
@@ -238,15 +238,15 @@ def download_image_data(
     Args:
         image_ids_or_dataset_id (list of string): Can be either a list with a single id (int) of a dataset or a list with images ids (int) or images ids prefixed by 'image-'
         dataset (bool, optional): Whether the image_ids_or_dataset_id is a dataset id and all images from this dataset should be retrieved (true) or image_ids_or_dataset_id are individual image ids (false). Defaults to False.
-        download_original (bool, optional): Whether the original file uploded to omero should be downloaded. Defaults to False.
+        download_original (bool, optional): Whether the original file uploded to omero should be downloaded (ignored if `download_full` is set to True). Defaults to False.
         download_full (bool, optional): Whether the full image (hyperstack) on omero should be written to TIFF. Defaults to False.
-        channel (string, optional): Channel name. Defaults to None.
-        z_stack (int, optional): Z stack (plane) index. Defaults to 0.
-        frame (int, optional): T frame index. Defaults to 0.
-        coord (tuple of int, optional): Coordinates of the top left or center of the region to crop. Defaults to (0, 0).
-        width (int, optional): Width of the region to crop. Defaults to 0.
-        height (int, optional): Height of the region to crop. Defaults to 0.
-        region_spec (str, optional): How the region is specified ('rectangle' = coord is top left or 'center' = the region is center). Defaults to "rectangle".
+        channel (string, optional): Channel name (ignored if `download_full` or `download_original` is set to True). Defaults to None.
+        z_stack (int, optional): Z stack (plane) index (ignored if `download_full` or `download_original` is set to True). Defaults to 0.
+        frame (int, optional): T frame index (ignored if `download_full` or `download_original` is set to True). Defaults to 0.
+        coord (tuple of int, optional): Coordinates of the top left or center of the region to crop (ignored if `download_full` or `download_original` is set to True). Defaults to (0, 0).
+        width (int, optional): Width of the region to crop (ignored if `download_full` or `download_original` is set to True). Defaults to 0.
+        height (int, optional): Height of the region to crop (ignored if `download_full` or `download_original` is set to True). Defaults to 0.
+        region_spec (str, optional): How the region is specified ('rectangle' = coord is top left or 'center' = the region is center, ignored if `download_full` or `download_original` is set to True). Defaults to "rectangle".
         skip_failed (bool, optional): Do not stop the downloads if one fails. Defaults to False.
         download_tar (bool, optional): Put all downloaded images into a tar file. Defaults to False.
         omero_host (str, optional): omero host url. Defaults to "idr.openmicroscopy.org".
@@ -587,25 +587,6 @@ def _center_to_ul(center_x, center_y, width, height):
         "for which to retrieve data (default: "
         "read ids from stdin).",
     )
-    p.add_argument(
-        "--download-original",
-        dest="download_original",
-        action="store_true",
-        help="download the original file uploaded to omero",
-    )
-    p.add_argument(
-        "--download-full",
-        dest="download_full",
-        action="store_true",
-        help="download the full image on omero",
-    )
-    p.add_argument(
-        "-c",
-        "--channel",
-        help="name of the channel to retrieve data for "
-        "(note: the first channel of each image will be downloaded if "
-        "left unspecified)",
-    )
     region = p.add_mutually_exclusive_group()
     region.add_argument(
         "--rectangle",
@@ -629,8 +610,42 @@ def _center_to_ul(center_x, center_y, width, height):
         "Note: Even values for width and height will be rounded down to "
         "the nearest odd number.",
     )
-    p.add_argument("-f", "--frame", type=int, default=0)
-    p.add_argument("-z", "--z-stack", type=int, default=0)
+    region.add_argument(
+        "--download-original",
+        dest="download_original",
+        action="store_true",
+        help="download the original file uploaded to omero",
+    )
+    region.add_argument(
+        "--download-full",
+        dest="download_full",
+        action="store_true",
+        help="download the full image on omero",
+    )
+    p.add_argument(
+        "-c",
+        "--channel",
+        help="name of the channel to retrieve data for "
+        "(note: the first channel of each image will be downloaded if "
+        "left unspecified), ignored with `--download-original` and "
+        "`--download-full`",
+    )
+    p.add_argument(
+        "-f",
+        "--frame",
+        type=int,
+        default=0,
+        help="index of the frame to retrive data for (first frame is 0),"
+        " ignored with `--download-original` and `--download-full`",
+    )
+    p.add_argument(
+        "-z",
+        "--z-stack",
+        type=int,
+        default=0,
+        help="index of the slice to retrive data for (first slice is 0),"
+        " ignored with `--download-original` and `--download-full`",
+    )
     p.add_argument("--skip-failed", action="store_true")
     p.add_argument("--download-tar", action="store_true")
     p.add_argument("-oh", "--omero-host", type=str, default="idr.openmicroscopy.org")

From c463311a8056f1adeb6599a4a44d4236981096fc Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 26 Sep 2024 10:51:46 +0200
Subject: [PATCH 10/15] remove libtiff dependency

---
 tools/idr_download/idr_download_by_ids.py  | 7 +------
 tools/idr_download/idr_download_by_ids.xml | 1 -
 2 files changed, 1 insertion(+), 7 deletions(-)

diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py
index bde548ac799..bd7d42e6264 100644
--- a/tools/idr_download/idr_download_by_ids.py
+++ b/tools/idr_download/idr_download_by_ids.py
@@ -8,7 +8,6 @@
 from tempfile import TemporaryDirectory
 
 import numpy
-from libtiff import TIFF
 from omero.cli import cli_login
 from omero.constants.namespaces import NSBULKANNOTATIONS
 from omero.gateway import BlitzGateway
@@ -532,11 +531,7 @@ def download_image_data(
 
                     if download_tar:
                         fname = os.path.join(tempdir, fname)
-                    try:
-                        tiff = TIFF.open(fname, mode="w")
-                        tiff.write_image(im_array)
-                    finally:
-                        tiff.close()
+                    imwrite(fname, im_array)
                     # move image into tarball
                     if download_tar:
                         archive.add(fname, os.path.basename(fname))
diff --git a/tools/idr_download/idr_download_by_ids.xml b/tools/idr_download/idr_download_by_ids.xml
index a56d4f9684d..31fe96c3514 100644
--- a/tools/idr_download/idr_download_by_ids.xml
+++ b/tools/idr_download/idr_download_by_ids.xml
@@ -20,7 +20,6 @@
     </edam_operations>
     <requirements>
         <requirement type="package" version="5.19.4">omero-py</requirement>
-        <requirement type="package" version="0.6.1">pylibtiff</requirement>
         <requirement type="package" version="2024.9.20">tifffile</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[

From 3d29c24dd45a3d69b784c8b5762d357eda4a4a7f Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 26 Sep 2024 13:13:23 +0200
Subject: [PATCH 11/15] improve docstrings

---
 tools/idr_download/idr_download_by_ids.py | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py
index bd7d42e6264..465f045fb24 100644
--- a/tools/idr_download/idr_download_by_ids.py
+++ b/tools/idr_download/idr_download_by_ids.py
@@ -15,9 +15,9 @@
 
 
 def warn(message, image_identifier, warn_skip=False):
-    """Print an error message to stderr and
-    - prefix with the image identifier
-    - suffix with 'Skipping download!' if warn_skip is True
+    """Print an error `message` to stderr and
+    - prefix with the `image_identifier`
+    - suffix with 'Skipping download!' if `warn_skip` is True
 
     Args:
         message (string): Message to print to stderr
@@ -39,7 +39,7 @@ def warn(message, image_identifier, warn_skip=False):
 
 
 def find_channel_index(image, channel_name):
-    """Identify the channel index from the image and the channel name
+    """Identify the channel index from the `image` and the `channel_name`
 
     Args:
         image (omero.gateway._ImageWrapper): image wrapper on which the channel should be identified
@@ -66,7 +66,7 @@ def find_channel_index(image, channel_name):
 
 
 def get_clipping_region(image, x, y, w, h):
-    """Check x,y and adjust w,h to image size to be able to crop the image with these coordinates
+    """Check `x`, `y` and adjust `w`, `h` to image size to be able to crop the `image` with these coordinates
 
     Args:
         image (omero.gateway._ImageWrapper): image wrapper on which region want to be cropped
@@ -109,7 +109,7 @@ def get_clipping_region(image, x, y, w, h):
 
 
 def confine_plane(image, z):
-    """Adjust/Confine z to be among the possible z for the image
+    """Adjust/Confine `z` to be among the possible z for the `image`
 
     Args:
         image (omero.gateway._ImageWrapper): image wrapper for which the z is adjusted
@@ -128,7 +128,7 @@ def confine_plane(image, z):
 
 
 def confine_frame(image, t):
-    """Adjust/Confine t to be among the possible t for the image
+    """Adjust/Confine `t` to be among the possible t for the `image`
 
     Args:
         image (omero.gateway._ImageWrapper): image wrapper for which the t is adjusted
@@ -147,7 +147,7 @@ def confine_frame(image, t):
 
 
 def get_image_array(image, tile, z, c, t):
-    """Get a 2D numpy array from an image wrapper for a given tile, z, c, t
+    """Get a 2D numpy array from an `image` wrapper for a given `tile`, `z`, `c`, `t`
 
     Args:
         image (omero.gateway._ImageWrapper): image wrapper from which values are taken
@@ -171,7 +171,7 @@ def get_image_array(image, tile, z, c, t):
 
 
 def get_full_image_array(image):
-    """Get a 5D numpy array with all values from an image wrapper
+    """Get a 5D numpy array with all values from an `image` wrapper
 
     Args:
         image (omero.gateway._ImageWrapper): image wrapper from which values are taken
@@ -232,7 +232,7 @@ def download_image_data(
        - a 2D cropped region or
        - a hyperstack written in a tiff file
        - the original image uploaded in omero
-      Optionally, th final file can be in a tar
+      Optionally, the final file can be in a tar
 
     Args:
         image_ids_or_dataset_id (list of string): Can be either a list with a single id (int) of a dataset or a list with images ids (int) or images ids prefixed by 'image-'
@@ -546,7 +546,7 @@ def download_image_data(
 
 
 def _center_to_ul(center_x, center_y, width, height):
-    """Convert the center coordinates, width, height to upper left coordinates, width, height
+    """Convert the center coordinates (`center_x`, `center_y`), `width`, `height` to upper left coordinates, width, height
 
     Args:
         center_x (int): x coordinate of center

From f3b73864fc34568226f758ef617ff124162692a0 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 26 Sep 2024 13:34:23 +0200
Subject: [PATCH 12/15] add typing

---
 tools/idr_download/idr_download_by_ids.py | 78 +++++++++++------------
 1 file changed, 39 insertions(+), 39 deletions(-)

diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py
index 465f045fb24..963dc0e94b0 100644
--- a/tools/idr_download/idr_download_by_ids.py
+++ b/tools/idr_download/idr_download_by_ids.py
@@ -10,11 +10,11 @@
 import numpy
 from omero.cli import cli_login
 from omero.constants.namespaces import NSBULKANNOTATIONS
-from omero.gateway import BlitzGateway
+from omero.gateway import BlitzGateway, _ImageWrapper
 from tifffile import imwrite
 
 
-def warn(message, image_identifier, warn_skip=False):
+def warn(message: str, image_identifier: str, warn_skip: bool = False) -> None:
     """Print an error `message` to stderr and
     - prefix with the `image_identifier`
     - suffix with 'Skipping download!' if `warn_skip` is True
@@ -38,11 +38,11 @@ def warn(message, image_identifier, warn_skip=False):
     )
 
 
-def find_channel_index(image, channel_name):
+def find_channel_index(image: _ImageWrapper, channel_name: str) -> int:
     """Identify the channel index from the `image` and the `channel_name`
 
     Args:
-        image (omero.gateway._ImageWrapper): image wrapper on which the channel should be identified
+        image (_ImageWrapper): image wrapper on which the channel should be identified
         channel_name (string): name of the channel to look for
 
     Returns:
@@ -65,11 +65,11 @@ def find_channel_index(image, channel_name):
     return -1
 
 
-def get_clipping_region(image, x, y, w, h):
+def get_clipping_region(image: _ImageWrapper, x: int, y: int, w: int, h: int) -> list[int]:
     """Check `x`, `y` and adjust `w`, `h` to image size to be able to crop the `image` with these coordinates
 
     Args:
-        image (omero.gateway._ImageWrapper): image wrapper on which region want to be cropped
+        image (_ImageWrapper): image wrapper on which region want to be cropped
         x (int): left x coordinate
         y (int): top y coordinate
         w (int): width
@@ -80,7 +80,7 @@ def get_clipping_region(image, x, y, w, h):
         ValueError: if the x or y coordinates are larger than the width or height of the image.
 
     Returns:
-        list of int: new x, y, width, height adjusted to the image
+        list[int]: new [x, y, width, height] adjusted to the image
     """
     # If the (x, y) coordinate falls outside the image boundaries, we
     # cannot just shift it because that would render the meaning of
@@ -108,11 +108,11 @@ def get_clipping_region(image, x, y, w, h):
     return [x, y, w, h]
 
 
-def confine_plane(image, z):
+def confine_plane(image: _ImageWrapper, z: int) -> int:
     """Adjust/Confine `z` to be among the possible z for the `image`
 
     Args:
-        image (omero.gateway._ImageWrapper): image wrapper for which the z is adjusted
+        image (_ImageWrapper): image wrapper for which the z is adjusted
         z (int): plane index that need to be confined
 
     Returns:
@@ -127,11 +127,11 @@ def confine_plane(image, z):
     return z
 
 
-def confine_frame(image, t):
+def confine_frame(image: _ImageWrapper, t: int) -> int:
     """Adjust/Confine `t` to be among the possible t for the `image`
 
     Args:
-        image (omero.gateway._ImageWrapper): image wrapper for which the t is adjusted
+        image (_ImageWrapper): image wrapper for which the t is adjusted
         t (int): frame index that need to be confined
 
     Returns:
@@ -146,18 +146,18 @@ def confine_frame(image, t):
     return t
 
 
-def get_image_array(image, tile, z, c, t):
+def get_image_array(image: _ImageWrapper, tile: list[int], z: int, c: int, t: int) -> numpy.ndarray:
     """Get a 2D numpy array from an `image` wrapper for a given `tile`, `z`, `c`, `t`
 
     Args:
-        image (omero.gateway._ImageWrapper): image wrapper from which values are taken
-        tile (list of int): [x, y, width, height] where x,y is the top left coordinate of the region to crop
+        image (_ImageWrapper): image wrapper from which values are taken
+        tile (list[int]): [x, y, width, height] where x,y is the top left coordinate of the region to crop
         z (int): plane index
         c (int): channel index
         t (int): frame index
 
     Returns:
-        numpy array of 2 dimensions: image values of the selected area
+        numpy.ndarray: image values of the selected area (2 dimensions)
     """
     pixels = image.getPrimaryPixels()
     try:
@@ -170,14 +170,14 @@ def get_image_array(image, tile, z, c, t):
     return selection
 
 
-def get_full_image_array(image):
+def get_full_image_array(image: _ImageWrapper) -> numpy.ndarray:
     """Get a 5D numpy array with all values from an `image` wrapper
 
     Args:
-        image (omero.gateway._ImageWrapper): image wrapper from which values are taken
+        image (_ImageWrapper): image wrapper from which values are taken
 
     Returns:
-        numpy array of 5 dimensions: image values in the TZCYX order
+        numpy.ndarray: image values in the TZCYX order (5 dimensions)
     """
     # The goal is to get the image in TZCYX order
     pixels = image.getPrimaryPixels()
@@ -209,23 +209,23 @@ def get_full_image_array(image):
 
 
 def download_image_data(
-    image_ids_or_dataset_id,
-    dataset=False,
-    download_original=False,
-    download_full=False,
-    channel=None,
-    z_stack=0,
-    frame=0,
-    coord=(0, 0),
-    width=0,
-    height=0,
-    region_spec="rectangle",
-    skip_failed=False,
-    download_tar=False,
-    omero_host="idr.openmicroscopy.org",
-    omero_secured=False,
-    config_file=None,
-):
+    image_ids_or_dataset_id: str,
+    dataset: bool = False,
+    download_original: bool = False,
+    download_full: bool = False,
+    channel: str = None,
+    z_stack: int = 0,
+    frame: int = 0,
+    coord: tuple[int, int] = (0, 0),
+    width: int = 0,
+    height: int = 0,
+    region_spec: str = "rectangle",
+    skip_failed: bool = False,
+    download_tar: bool = False,
+    omero_host: str = "idr.openmicroscopy.org",
+    omero_secured: bool = False,
+    config_file: str = None,
+) -> None:
     """Download the image data of
       either a list of image ids or all images from a dataset.
       The image data can be:
@@ -235,14 +235,14 @@ def download_image_data(
       Optionally, the final file can be in a tar
 
     Args:
-        image_ids_or_dataset_id (list of string): Can be either a list with a single id (int) of a dataset or a list with images ids (int) or images ids prefixed by 'image-'
+        image_ids_or_dataset_id (list[str]): Can be either a list with a single id (int) of a dataset or a list with images ids (int) or images ids prefixed by 'image-'
         dataset (bool, optional): Whether the image_ids_or_dataset_id is a dataset id and all images from this dataset should be retrieved (true) or image_ids_or_dataset_id are individual image ids (false). Defaults to False.
         download_original (bool, optional): Whether the original file uploded to omero should be downloaded (ignored if `download_full` is set to True). Defaults to False.
         download_full (bool, optional): Whether the full image (hyperstack) on omero should be written to TIFF. Defaults to False.
         channel (string, optional): Channel name (ignored if `download_full` or `download_original` is set to True). Defaults to None.
         z_stack (int, optional): Z stack (plane) index (ignored if `download_full` or `download_original` is set to True). Defaults to 0.
         frame (int, optional): T frame index (ignored if `download_full` or `download_original` is set to True). Defaults to 0.
-        coord (tuple of int, optional): Coordinates of the top left or center of the region to crop (ignored if `download_full` or `download_original` is set to True). Defaults to (0, 0).
+        coord (tuple[int, int], optional): Coordinates of the top left or center of the region to crop (ignored if `download_full` or `download_original` is set to True). Defaults to (0, 0).
         width (int, optional): Width of the region to crop (ignored if `download_full` or `download_original` is set to True). Defaults to 0.
         height (int, optional): Height of the region to crop (ignored if `download_full` or `download_original` is set to True). Defaults to 0.
         region_spec (str, optional): How the region is specified ('rectangle' = coord is top left or 'center' = the region is center, ignored if `download_full` or `download_original` is set to True). Defaults to "rectangle".
@@ -545,7 +545,7 @@ def download_image_data(
                         raise
 
 
-def _center_to_ul(center_x, center_y, width, height):
+def _center_to_ul(center_x: int, center_y: int, width: int, height: int) -> list[int]:
     """Convert the center coordinates (`center_x`, `center_y`), `width`, `height` to upper left coordinates, width, height
 
     Args:
@@ -555,7 +555,7 @@ def _center_to_ul(center_x, center_y, width, height):
         height (int): height
 
     Returns:
-        list of 4 int: x, y, width, height where x,y are the upper left coordinates
+        list[int]: [x, y, width, height] where x,y are the upper left coordinates
     """
     if width > 0:
         ext_x = (width - 1) // 2

From 902d6f92b38836abf76b5a8a6f7cc5b8fa47c3cf Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 26 Sep 2024 13:35:19 +0200
Subject: [PATCH 13/15] run black

---
 tools/idr_download/idr_download_by_ids.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py
index 963dc0e94b0..2892df4ebe8 100644
--- a/tools/idr_download/idr_download_by_ids.py
+++ b/tools/idr_download/idr_download_by_ids.py
@@ -65,7 +65,9 @@ def find_channel_index(image: _ImageWrapper, channel_name: str) -> int:
     return -1
 
 
-def get_clipping_region(image: _ImageWrapper, x: int, y: int, w: int, h: int) -> list[int]:
+def get_clipping_region(
+    image: _ImageWrapper, x: int, y: int, w: int, h: int
+) -> list[int]:
     """Check `x`, `y` and adjust `w`, `h` to image size to be able to crop the `image` with these coordinates
 
     Args:
@@ -146,7 +148,9 @@ def confine_frame(image: _ImageWrapper, t: int) -> int:
     return t
 
 
-def get_image_array(image: _ImageWrapper, tile: list[int], z: int, c: int, t: int) -> numpy.ndarray:
+def get_image_array(
+    image: _ImageWrapper, tile: list[int], z: int, c: int, t: int
+) -> numpy.ndarray:
     """Get a 2D numpy array from an `image` wrapper for a given `tile`, `z`, `c`, `t`
 
     Args:

From c255347182d5877e32997c8189a86479a08aee30 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 26 Sep 2024 13:36:24 +0200
Subject: [PATCH 14/15] fix warn I introduced

---
 tools/idr_download/idr_download_by_ids.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py
index 2892df4ebe8..70b7c8ff9c3 100644
--- a/tools/idr_download/idr_download_by_ids.py
+++ b/tools/idr_download/idr_download_by_ids.py
@@ -205,8 +205,7 @@ def get_full_image_array(image: _ImageWrapper) -> numpy.ndarray:
         )
     except Exception as e:
         warning = "{0} (ID: {1})".format(image.getName(), image.getId())
-        warn("Could not download the requested region", warning)
-        warn(e.msg)
+        warn(f"Could not download the full image \n {e.msg}", warning)
         return
 
     return all_planes_reshaped

From edceaaff2891854d44bb42344533b3c5d07e3338 Mon Sep 17 00:00:00 2001
From: Lucille Delisle <lucille.delisle@epfl.ch>
Date: Thu, 26 Sep 2024 13:41:14 +0200
Subject: [PATCH 15/15] fix linting

---
 tools/idr_download/idr_download_by_ids.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py
index 70b7c8ff9c3..bae7da3a5ec 100644
--- a/tools/idr_download/idr_download_by_ids.py
+++ b/tools/idr_download/idr_download_by_ids.py
@@ -10,7 +10,7 @@
 import numpy
 from omero.cli import cli_login
 from omero.constants.namespaces import NSBULKANNOTATIONS
-from omero.gateway import BlitzGateway, _ImageWrapper
+from omero.gateway import _ImageWrapper, BlitzGateway
 from tifffile import imwrite