copick-utils 1.1.0__tar.gz → 1.2.0__tar.gz

copick_utils-1.2.0/.release-please.manifest.json

@@ -0,0 +1,3 @@
+{
+  ".": "1.2.0"
+}

{copick_utils-1.1.0 → copick_utils-1.2.0}/CHANGELOG.md

@@ -1,5 +1,17 @@
 # Changelog
 
+## [1.2.0](https://github.com/copick/copick-utils/compare/copick-utils-v1.1.0...copick-utils-v1.2.0) (2026-01-31)
+
+
+### ✨ Features
+
+* add parser uri to readers, add function to download portal project fo… ([#43](https://github.com/copick/copick-utils/issues/43)) ([7743ee5](https://github.com/copick/copick-utils/commit/7743ee5facb6dff037f8348852c6edcd105abe25))
+
+
+### 🐞 Bug Fixes
+
+* URI in copick readers ([#45](https://github.com/copick/copick-utils/issues/45)) ([926f01d](https://github.com/copick/copick-utils/commit/926f01dfccb537bca90fd30ee59ceacb83d7f947))
+
 ## [1.1.0](https://github.com/copick/copick-utils/compare/copick-utils-v1.0.2...copick-utils-v1.1.0) (2026-01-26)
 
 

{copick_utils-1.1.0 → copick_utils-1.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: copick-utils
-Version: 1.1.0
+Version: 1.2.0
 Summary: Utilities for copick
 Project-URL: Repository, https://github.com/KyleHarrington/copick-utils.git
 Project-URL: Issues, https://github.com/KyleHarrington/copick-utils/issues
@@ -33,6 +33,7 @@ Requires-Dist: click-option-group
 Requires-Dist: copick>=1.16.0
 Requires-Dist: manifold3d
 Requires-Dist: mapbox-earcut
+Requires-Dist: mdocfile
 Requires-Dist: numpy
 Requires-Dist: rtree
 Requires-Dist: scikit-image

{copick_utils-1.1.0 → copick_utils-1.2.0}/pyproject.toml

@@ -29,6 +29,7 @@ dependencies = [
     "trimesh",
     "manifold3d",
     "mapbox-earcut",
+    "mdocfile",
     "tqdm",
     "scikit-learn",
     "shapely",
@@ -88,6 +89,9 @@ clippicks = "copick_utils.cli.logical_commands:clippicks"
 picksin = "copick_utils.cli.logical_commands:picksin"
 picksout = "copick_utils.cli.logical_commands:picksout"
 
+[project.entry-points."copick.download.commands"]
+project = "copick_utils.cli.download_commands:project"
+
 [tool.hatch.version]
 path = "src/copick_utils/__init__.py"
 

{copick_utils-1.1.0 → copick_utils-1.2.0}/src/copick_utils/__init__.py

@@ -1,4 +1,4 @@
 # SPDX-FileCopyrightText: 2024-present Kyle Harrington <czi@kyleharrington.com>
 #
 # SPDX-License-Identifier: MIT
-__version__ = "1.1.0"
+__version__ = "1.2.0"

copick_utils-1.2.0/src/copick_utils/cli/download.py

@@ -0,0 +1,34 @@
+import click
+
+
+@click.command(
+    context_settings={"show_default": True},
+    short_help="Download tilt series and alignments from the CryoET Data Portal.",
+    no_args_is_help=True,
+)
+@click.option(
+    "-ds",
+    "--dataset",
+    required=True,
+    type=str,
+    help="Dataset ID to download from the CryoET Data Portal.",
+)
+@click.option(
+    "-o",
+    "--output",
+    required=True,
+    default=".",
+    type=str,
+    help="Output directory to save the downloaded files.",
+)
+def project(dataset: str, output: str):
+    """
+    Download tilt series and alignments from the CryoET Data Portal for sub-tomogram averaging with py2rely.
+    """
+    download_project(dataset, output)
+
+
+def download_project(dataset: str, output: str):
+    import copick_utils.io.portal as portal
+
+    portal.download_aretomo_files(dataset, output)

copick_utils-1.2.0/src/copick_utils/cli/download_commands.py

@@ -0,0 +1,11 @@
+"""CLI commands for downloading data from the CryoET Data Portal.
+
+This module imports all download commands from specialized files for better organization.
+"""
+
+from copick_utils.cli.download import project
+
+# All commands are now available for import by the main CLI
+__all__ = [
+    "project",
+]

copick_utils-1.2.0/src/copick_utils/io/portal.py

@@ -0,0 +1,149 @@
+"""
+A minimal example using minimal libraries / imports to download relevant AreTomo files
+from the CryoET Data Portal. Downloads the corresponding files, using the run ID as the
+base filename.
+
+Original implementation by Daniel Ji and Utz Ermel.
+"""
+import multiprocessing
+import os
+
+import cryoet_data_portal as cdp
+import mdocfile
+import numpy as np
+import pandas as pd
+import requests
+import s3fs
+
+global_client = cdp.Client()
+
+
+def download_aretomo_files(dataset_id: int, output_dir: str):
+    print(f"Fetching tiltseries for dataset id {dataset_id}...", flush=True)
+    tiltseries_list: list[cdp.TiltSeries] = [
+        tiltseries for run in cdp.Dataset.get_by_id(global_client, dataset_id).runs for tiltseries in run.tiltseries
+    ]  # a bit slow for some reason, can take some time
+    tiltseries_run_ids_and_ts_ids = [(ts.run.id, ts.id) for ts in tiltseries_list]
+    print(
+        f"Found {len(tiltseries_run_ids_and_ts_ids)} tiltseries for dataset id {dataset_id}. Starting downloads...",
+        flush=True,
+    )
+    with multiprocessing.Pool(processes=8) as pool:  # adjust number of processes as needed
+        for _ in pool.imap_unordered(
+            _worker_download_aretomo_files_for_tiltseries,
+            [
+                (dataset_id, run_name, output_dir, tiltseries_id)
+                for run_name, tiltseries_id in tiltseries_run_ids_and_ts_ids
+            ],
+        ):
+            pass
+
+
+def _worker_download_aretomo_files_for_tiltseries(args):
+    dataset_id, run_name, output_dir, tiltseries_id = args
+    download_aretomo_files_for_tiltseries(dataset_id, run_name, output_dir, tiltseries_id)
+
+
+# note: this function assumes that there is only one tiltseries per run
+# note: the tiltseries name is equivlaent to the run name
+# if tiltseries_id is provided, will be prioritized over dataset_id + run_name
+def download_aretomo_files_for_tiltseries(dataset_id: int, run_name: str, output_dir: str, tiltseries_id: int = None):
+    print(f"[{run_name}] Downloading AreTomo files for tiltseries id {tiltseries_id}...", flush=True)
+
+    client = cdp.Client()
+    s3 = s3fs.S3FileSystem(anon=True)
+    if not tiltseries_id:
+        all_tiltseries = cdp.TiltSeries.find(
+            client,
+            query_filters=[cdp.TiltSeries.run.dataset_id == dataset_id, cdp.TiltSeries.run.name == run_name],
+        )
+        if len(all_tiltseries) == 0:
+            raise ValueError(f"No tiltseries found for dataset_id {dataset_id} and run_name {run_name}")
+        if len(all_tiltseries) > 1:
+            raise ValueError(f"Multiple tiltseries found for dataset_id {dataset_id} and run_name {run_name}")
+        tiltseries = all_tiltseries[0]
+    else:
+        tiltseries = cdp.TiltSeries.get_by_id(client, tiltseries_id)
+
+    # get the s3 folder path and then glob for *.tlt / *.rawtlt files to download them, renaming the base to match the run id
+    s3_folder_path = tiltseries.s3_mrc_file.rsplit("/", 1)[0] + "/"
+    tlt_files = s3.glob(s3_folder_path + "*.tlt") + s3.glob(s3_folder_path + "*.rawtlt")
+    for tlt_file in tlt_files:
+        base_name = os.path.basename(tlt_file)
+        ext = os.path.splitext(base_name)[1]
+        dest_file = os.path.join(output_dir, f"{tiltseries.run.id}{ext}")
+        s3.get(tlt_file, dest_file)
+        print(f"[{tiltseries.run.id}] Downloaded {base_name} as {os.path.basename(dest_file)}.", flush=True)
+
+    # do the same for "*CTF*.txt" files and "*ctf*.txt" files
+    ctf_files = s3.glob(s3_folder_path + "*CTF*.txt") + s3.glob(s3_folder_path + "*ctf*.txt")
+    if len(ctf_files) == 0:
+        print(f"WARNING: No CTF files found for tiltseries id {tiltseries.id}")
+    else:
+        ctf_file = ctf_files[0]
+        base_name = os.path.basename(ctf_file)
+        if len(ctf_files) > 1:
+            print(f"WARNING: Multiple CTF files found for tiltseries id {tiltseries.id}, using {base_name}")
+        ext = os.path.splitext(base_name)[1]
+        dest_file = os.path.join(output_dir, f"{tiltseries.run.id}_CTF.txt")
+        s3.get(ctf_file, dest_file)
+        print(f"[{tiltseries.run.id}] Downloaded {base_name} as {os.path.basename(dest_file)}.", flush=True)
+
+    # now find the corresponding alignment for this tiltseries and download the "*.aln" file
+    if len(tiltseries.alignments) == 0:
+        print(f"WARNING: No alignments found for tiltseries id {tiltseries.id}")
+    elif len(tiltseries.alignments) > 1:
+        print(f"WARNING: Multiple alignments found for tiltseries id {tiltseries.id}")
+    else:
+        alignment = tiltseries.alignments[0]
+        s3_alignment_folder_path = alignment.s3_alignment_metadata.rsplit("/", 1)[0] + "/"
+        aln_files = s3.glob(s3_alignment_folder_path + "*.aln")
+        if len(aln_files) == 0:
+            raise ValueError(f"No .aln files found for run name {tiltseries.run.name} and alignment id {alignment.id}")
+        aln_file = aln_files[0]
+        base_name = os.path.basename(aln_file)
+        if len(aln_files) > 1:
+            print(f"WARNING: Multiple .aln files found for run name {tiltseries.run.name}, using {base_name}")
+        ext = os.path.splitext(base_name)[1]
+        dest_file = os.path.join(output_dir, f"{tiltseries.run.id}{ext}")
+        s3.get(aln_file, dest_file)
+        print(f"[{tiltseries.run.id}] Downloaded {base_name} as {os.path.basename(dest_file)}.", flush=True)
+
+    # now get the mdoc file from the Frames/ folder
+    frames = tiltseries.run.frames
+    if len(frames) == 0:
+        raise ValueError(f"No frames found for run name {tiltseries.run.name}")
+    frame = frames[0]
+    s3_frames_folder_path = frame.s3_frame_path.rsplit("/", 1)[0] + "/"
+    mdoc_files = s3.glob(s3_frames_folder_path + "*.mdoc")
+    if len(mdoc_files) == 0:
+        raise ValueError(f"No .mdoc files found for run name {tiltseries.run.name}")
+    mdoc_file = mdoc_files[0]
+    base_name = os.path.basename(mdoc_file)
+    if len(mdoc_files) > 1:
+        print(f"WARNING: Multiple .mdoc files found for run name {tiltseries.run.name}, using {base_name}")
+    ext = os.path.splitext(base_name)[1]
+    dest_file = os.path.join(output_dir, f"{tiltseries.run.id}{ext}")
+    s3.get(mdoc_file, dest_file)
+    print(f"[{tiltseries.run.id}] Downloaded {base_name} as {os.path.basename(dest_file)}.", flush=True)
+
+    # download tiltseries mrc file
+    tiltseries_file = os.path.join(output_dir, f"{tiltseries.run.id}.mrc")
+    tiltseries_url = tiltseries.https_mrc_file
+    response = requests.get(tiltseries_url, stream=True)
+    response.raise_for_status()
+    with open(tiltseries_file, "wb") as f:
+        for chunk in response.iter_content(chunk_size=8192):
+            f.write(chunk)
+    print(f"[{tiltseries.run.id}] Downloaded tiltseries mrc file as {os.path.basename(tiltseries_file)}.", flush=True)
+
+    # create imod file for order list
+    mdoc = mdocfile.read(os.path.join(output_dir, f"{tiltseries.run.id}.mdoc"))
+    order_list = mdoc["TiltAngle"]
+    imodpath = os.path.join(output_dir, f"{tiltseries.run.id}_Imod")
+    os.makedirs(imodpath, exist_ok=True)
+    number = np.arange(len(order_list)) + 1
+
+    # save in csv with 'ImageNumber', 'TiltAngle' headers
+    df = pd.DataFrame({"ImageNumber": number, "TiltAngle": order_list})
+    df.to_csv(os.path.join(imodpath, f"{tiltseries.run.id}_order_list.csv"), index=False)

copick_utils-1.2.0/src/copick_utils/io/readers.py

@@ -0,0 +1,200 @@
+import numpy as np
+from copick.util.uri import resolve_copick_objects
+
+
+def tomogram(run, voxel_size: float = 10, algorithm: str = "wbp", raise_error: bool = False, verbose=True):
+    """
+    Reads a tomogram from a Copick run.
+
+    Parameters:
+    -----------
+    run: copick.Run
+    voxel_size: float
+    algorithm: str
+    raise_error: bool
+    verbose: bool
+    Returns:
+    --------
+    vol: np.ndarray - The tomogram.
+    """
+
+    # Get the tomogram from the Copick URI
+    try:
+        uri = f"{algorithm}@{voxel_size}"
+        vol = resolve_copick_objects(uri, run.root, "tomogram", run_name=run.name)
+        return vol[0].numpy()
+    except Exception as err:  # Report which orbject is missing
+        # Try to resolve the tomogram using the Copick URI
+        voxel_spacing_obj = run.get_voxel_spacing(voxel_size)
+
+        if voxel_spacing_obj is None:
+            # Query Avaiable Voxel Spacings
+            availableVoxelSpacings = [tomo.voxel_size for tomo in run.voxel_spacings]
+
+            # Report to the user which voxel spacings they can use
+            message = (
+                f"[Warning] No tomogram found for {run.name} with uri: {uri}\n"
+                f"Available voxel sizes are: {', '.join(map(str, availableVoxelSpacings))}"
+            )
+            if raise_error:
+                raise ValueError(message) from err
+            elif verbose:
+                print(message)
+            return None
+
+        tomogram = voxel_spacing_obj.get_tomogram(algorithm)
+        if tomogram is None:
+            # Get available algorithms
+            availableAlgorithms = [tomo.tomo_type for tomo in run.get_voxel_spacing(voxel_size).tomograms]
+
+            # Report to the user which algorithms are available
+            message = (
+                f"[Warning] No tomogram found for {run.name} with uri: {uri}\n"
+                f"Available algorithms @{voxel_size}A are: {', '.join(availableAlgorithms)}"
+            )
+            if raise_error:
+                raise ValueError(message) from err
+            elif verbose:
+                print(message)
+            return None
+
+
+def segmentation(run, voxel_spacing: float, name: str, user_id=None, session_id=None, raise_error=False, verbose=True):
+    """
+    Reads a segmentation from a Copick run.
+
+    Parameters:
+    -----------
+    run: copick.Run
+    voxel_spacing: float
+    name: str
+    user_id: str
+    session_id: str
+    raise_error: bool
+    verbose: bool
+    Returns:
+    --------
+    seg: np.ndarray - The segmentation.
+    """
+
+    # Construct the Target URI
+    if session_id is None and user_id is None:
+        uri = f"{name}@{voxel_spacing}"
+    elif session_id is None:
+        uri = f"{name}:{user_id}@{voxel_spacing}"
+    else:
+        uri = f"{name}:{user_id}/{session_id}@{voxel_spacing}"
+
+    # Try to resolve the segmentation using the Copick URI
+    try:
+        segs = resolve_copick_objects(uri, run.root, "segmentation", run_name=run.name)
+        return segs[0].numpy()
+    except Exception as err:
+        # Force the voxel spacing to be a float
+        voxel_spacing = float(voxel_spacing)
+
+        # Get all available segmentations with their metadata
+        available_segs = run.get_segmentations(voxel_size=voxel_spacing)
+
+        if len(available_segs) == 0:
+            available_segs = run.get_segmentations()
+            message = (
+                f"No segmentation found for URI: {uri}\n"
+                f"Available segmentations avaiable w/following voxel sizes: {', '.join(map(str, [s.voxel_size for s in available_segs]))}"
+            )
+        else:
+            seg_info = [(s.name, s.user_id, s.session_id) for s in available_segs]
+
+            # Format the information for display
+            seg_details = [f"(name: {name}, user_id: {uid}, session_id: {sid})" for name, uid, sid in seg_info]
+
+            message = (
+                f"\nNo segmentation at {voxel_spacing} A found matching:\n"
+                f"  name: {name}, user_id: {user_id}, session_id: {session_id}\n"
+                f"Available segmentations in {run.name} are:\n  " + "\n  ".join(seg_details)
+            )
+        if raise_error:
+            raise ValueError(message) from err
+        elif verbose:
+            print(message)
+        else:
+            return None
+
+
+def coordinates(
+    run,  # CoPick run object containing the segmentation data
+    name: str,  # Name of the object or protein for which coordinates are being extracted
+    user_id: str,  # Identifier of the user that generated the picks
+    session_id: str = None,  # Identifier of the session that generated the picks
+    voxel_size: float = 10,  # Voxel size of the tomogram, used for scaling the coordinates
+    raise_error: bool = False,
+    verbose: bool = True,
+):
+    """
+    Reads the coordinates of the picks from a Copick run.
+
+    Parameters:
+    -----------
+    run: copick.Run
+    name: str
+    user_id: str
+    session_id: str
+    voxel_size: float
+    raise_error: bool
+    verbose: bool
+
+    Returns:
+    --------
+    coordinates: np.ndarray - The 3D coordinates of the picks in voxel space.
+    """
+    # Retrieve the pick points associated with the specified object and user ID
+    picks = run.get_picks(object_name=name, user_id=user_id, session_id=session_id)
+
+    if len(picks) == 0:
+        # Get all available segmentations with their metadata
+
+        available_picks = run.get_picks()
+        picks_info = [(s.pickable_object_name, s.user_id, s.session_id) for s in available_picks]
+
+        # Format the information for display
+        picks_details = [f"(name: {name}, user_id: {uid}, session_id: {sid})" for name, uid, sid in picks_info]
+
+        message = (
+            f"\nNo picks found matching:\n"
+            f"  name: {name}, user_id: {user_id}, session_id: {session_id}\n"
+            f"Available picks are:\n  " + "\n  ".join(picks_details)
+        )
+        if raise_error:
+            raise ValueError(message)
+        elif verbose:
+            print(message)
+        return None
+
+    elif len(picks) > 1:
+        # Format pick information for display
+        picks_info = [(p.pickable_object_name, p.user_id, p.session_id) for p in picks]
+        picks_details = [f"(name: {name}, user_id: {uid}, session_id: {sid})" for name, uid, sid in picks_info]
+
+        if verbose:
+            print(
+                "[Warning] More than 1 pick is available for the query information."
+                "\nAvailable picks are:\n  " + "\n  ".join(picks_details) + f"\n"
+                f"Defaulting to loading:\n {picks[0]}\n",
+            )
+
+    points = picks[0].points
+
+    # Initialize an array to store the coordinates
+    nPoints = len(picks[0].points)  # Number of points retrieved
+    coordinates = np.zeros([len(picks[0].points), 3])  # Create an empty array to hold the (z, y, x) coordinates
+
+    # Iterate over all points and convert their locations to coordinates in voxel space
+    for ii in range(nPoints):
+        coordinates[ii,] = [
+            points[ii].location.z / voxel_size,  # Scale z-coordinate by voxel size
+            points[ii].location.y / voxel_size,  # Scale y-coordinate by voxel size
+            points[ii].location.x / voxel_size,
+        ]  # Scale x-coordinate by voxel size
+
+    # Return the array of coordinates
+    return coordinates

{copick_utils-1.1.0 → copick_utils-1.2.0}/src/copick_utils/io/writers.py

@@ -28,17 +28,17 @@ def tomogram(run, input_volume, voxel_size=10, algorithm="wbp"):
         voxel_spacing = run.new_voxel_spacing(voxel_size=voxel_size)
 
     # Check if We Need to Create a New Tomogram for Given Algorithm
-    tomogram = voxel_spacing.get_tomogram(algorithm)
-    if tomogram is None:
-        tomogram = voxel_spacing.new_tomogram(tomo_type=algorithm)
+    tomo = voxel_spacing.get_tomogram(algorithm)
+    if tomo is None:
+        tomo = voxel_spacing.new_tomogram(tomo_type=algorithm)
 
     # Write the tomogram data
-    tomogram.from_numpy(input_volume)
+    tomo.from_numpy(input_volume)
 
 
 def segmentation(
     run,
-    segmentation_volume,
+    seg_vol,
     user_id,
     name="segmentation",
     session_id="0",
@@ -52,7 +52,7 @@ def segmentation(
     -----------
     run : copick.Run
         The current Copick run object.
-    segmentation_volume : np.ndarray
+    seg_vol : np.ndarray
         The segmentation data to be written.
     user_id : str
         The ID of the user creating the segmentation.
@@ -76,7 +76,7 @@ def segmentation(
 
     # If no segmentation exists or no segmentation at the given voxel size, create a new one
     if len(segmentations) == 0 or any(seg.voxel_size != voxel_size for seg in segmentations):
-        segmentation = run.new_segmentation(
+        seg = run.new_segmentation(
             voxel_size=voxel_size,
             name=name,
             session_id=session_id,
@@ -85,7 +85,7 @@ def segmentation(
         )
     else:
         # Overwrite the current segmentation at the specified voxel size if it exists
-        segmentation = next(seg for seg in segmentations if seg.voxel_size == voxel_size)
+        seg = next(seg for seg in segmentations if seg.voxel_size == voxel_size)
 
     # Write the segmentation data
-    segmentation.from_numpy(segmentation_volume, dtype=np.uint8)
+    seg.from_numpy(seg_vol, dtype=np.uint8)

copick_utils-1.1.0/.release-please.manifest.json

@@ -1,3 +0,0 @@
-{
-  ".": "1.1.0"
-}

copick_utils-1.1.0/src/copick_utils/io/readers.py

@@ -1,135 +0,0 @@
-import numpy as np
-
-
-def tomogram(run, voxel_size: float = 10, algorithm: str = "wbp", raise_error: bool = False):
-    voxel_spacing_obj = run.get_voxel_spacing(voxel_size)
-
-    if voxel_spacing_obj is None:
-        # Query Avaiable Voxel Spacings
-        availableVoxelSpacings = [tomo.voxel_size for tomo in run.voxel_spacings]
-
-        # Report to the user which voxel spacings they can use
-        message = (
-            f"[Warning] No tomogram found for {run.name} with voxel size {voxel_size} and tomogram type {algorithm}"
-            f"Available spacings are: {', '.join(map(str, availableVoxelSpacings))}"
-        )
-        if raise_error:
-            raise ValueError(message)
-        else:
-            print(message)
-            return None
-
-    tomogram = voxel_spacing_obj.get_tomogram(algorithm)
-    if tomogram is None:
-        # Get available algorithms
-        availableAlgorithms = [tomo.tomo_type for tomo in run.get_voxel_spacing(voxel_size).tomograms]
-
-        # Report to the user which algorithms are available
-        message = (
-            f"[Warning] No tomogram found for {run.name} with voxel size {voxel_size} and tomogram type {algorithm}"
-            f"Available algorithms are: {', '.join(availableAlgorithms)}"
-        )
-        if raise_error:
-            raise ValueError(message)
-        else:
-            print(message)
-            return None
-
-    return tomogram.numpy()
-
-
-def segmentation(run, voxel_spacing: float, segmentation_name: str, session_id=None, user_id=None, raise_error=False):
-    seg = run.get_segmentations(
-        name=segmentation_name,
-        session_id=session_id,
-        user_id=user_id,
-        voxel_size=voxel_spacing,
-    )
-
-    # No Segmentations Are Available, Result in Error
-    if len(seg) == 0:
-        # Get all available segmentations with their metadata
-        available_segs = run.get_segmentations(voxel_size=voxel_spacing)
-        seg_info = [(s.name, s.user_id, s.session_id) for s in available_segs]
-
-        # Format the information for display
-        seg_details = [f"(name: {name}, user_id: {uid}, session_id: {sid})" for name, uid, sid in seg_info]
-
-        message = (
-            f"\nNo segmentation found matching:\n"
-            f"  name: {segmentation_name}, user_id: {user_id}, session_id: {session_id}\n"
-            f"Available segmentations in {run.name} are:\n  " + "\n  ".join(seg_details)
-        )
-        if raise_error:
-            raise ValueError(message)
-        else:
-            print(message)
-            return None
-
-    # No Segmentations Are Available, Result in Error
-    if len(seg) > 1:
-        print(
-            f"[Warning] More Than 1 Segmentation is Available for the Query Information. "
-            f"Available Segmentations are: {seg} "
-            f"Defaulting to Loading: {seg[0]}\n",
-        )
-    seg = seg[0]
-
-    return seg.numpy()
-
-
-def coordinates(
-    run,  # CoPick run object containing the segmentation data
-    name: str,  # Name of the object or protein for which coordinates are being extracted
-    user_id: str,  # Identifier of the user that generated the picks
-    session_id: str = None,  # Identifier of the session that generated the picks
-    voxel_size: float = 10,  # Voxel size of the tomogram, used for scaling the coordinates
-    raise_error: bool = False,
-):
-    # Retrieve the pick points associated with the specified object and user ID
-    picks = run.get_picks(object_name=name, user_id=user_id, session_id=session_id)
-
-    if len(picks) == 0:
-        # Get all available segmentations with their metadata
-
-        available_picks = run.get_picks()
-        picks_info = [(s.pickable_object_name, s.user_id, s.session_id) for s in available_picks]
-
-        # Format the information for display
-        picks_details = [f"(name: {name}, user_id: {uid}, session_id: {sid})" for name, uid, sid in picks_info]
-
-        message = (
-            f"\nNo picks found matching:\n"
-            f"  name: {name}, user_id: {user_id}, session_id: {session_id}\n"
-            f"Available picks are:\n  " + "\n  ".join(picks_details)
-        )
-        if raise_error:
-            raise ValueError(message)
-        else:
-            print(message)
-            return None
-    elif len(picks) > 1:
-        # Format pick information for display
-        picks_info = [(p.pickable_object_name, p.user_id, p.session_id) for p in picks]
-        picks_details = [f"(name: {name}, user_id: {uid}, session_id: {sid})" for name, uid, sid in picks_info]
-
-        print(
-            "[Warning] More than 1 pick is available for the query information."
-            "\nAvailable picks are:\n  " + "\n  ".join(picks_details) + f"\nDefaulting to loading:\n {picks[0]}\n",
-        )
-    points = picks[0].points
-
-    # Initialize an array to store the coordinates
-    nPoints = len(picks[0].points)  # Number of points retrieved
-    coordinates = np.zeros([len(picks[0].points), 3])  # Create an empty array to hold the (z, y, x) coordinates
-
-    # Iterate over all points and convert their locations to coordinates in voxel space
-    for ii in range(nPoints):
-        coordinates[ii,] = [
-            points[ii].location.z / voxel_size,  # Scale z-coordinate by voxel size
-            points[ii].location.y / voxel_size,  # Scale y-coordinate by voxel size
-            points[ii].location.x / voxel_size,
-        ]  # Scale x-coordinate by voxel size
-
-    # Return the array of coordinates
-    return coordinates