Python interface

ascent/ascent/cli.py

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+import mimetypes
+import os
+from pathlib import Path
+
+import click
+import girder_client
+
+# TODO
+# Update existing folder
+#  - require id
+# -update/overwrite
+# Support tags
+# -option for upload and update
+# Large image
+
+supportedVideoTypes = [
+  'video/mp4',
+  'video/webm',
+  'video/ogg',
+]
+supportedImageTypes = [
+  'image/apng',
+  'image/avif',
+  'image/bmp',
+  'image/gif',
+  'image/jpeg',
+  'image/png',
+  'image/tiff',
+  'image/webp',
+]
+
+_global_options = [
+    click.option(
+        "--port",
+        type=int,
+        help="Provide port that DIVE is running on. Default 8010",
+    ),
+    click.option(
+        "--url",
+        type=str,
+        help="Provide api URL. Defaults to 'localhost'"
+    )
+]
+
+
+def global_options(func):
+    for option in _global_options:
+        func = option(func)
+    return func
+
+
+_upload_arguments = [
+    click.argument(
+        "folder-name",
+        type=str,
+        required=True,
+    ),
+    click.argument(
+        "path",
+        required=True,
+        type=click.Path(exists=True, readable=True, path_type=Path),
+    ),
+
+]
+
+
+def upload_arguments(func):
+    for option in _upload_arguments:
+        func = option(func)
+    return func
+
+
+_upload_options = [
+    click.option(
+        "--parent-folder-id",
+        type=str,
+        help="The _id of girder folder that the new folder will be created in. Defaults to user root."
+    ),
+    click.option(
+        "--annotations-path",
+        type=click.Path(exists=True, readable=True, path_type=Path),
+        help="Local path for corresponding annotations file to be uploaded."
+
+    )
+
+]
+
+
+def upload_options(func):
+    for option in _upload_options:
+        func = option(func)
+    return func
+
+
+apiURL = "localhost"
+
+
+def login(api, port):
+
+    gc = girder_client.GirderClient(
+        api,
+        port=port,
+        apiRoot="girder/api/v1"
+      )
+    if not os.environ.get('DIVE_USER') or not os.environ.get('DIVE_PW'):
+        gc.authenticate(interactive=True)
+    else:
+        gc.authenticate(os.environ.get('DIVE_USER'), os.environ.get('DIVE_PW'))
+    return gc
+
+
+def create_folder(parent_folder, folder_name, gc):
+    new_folder = None
+    try:
+        if parent_folder:
+            new_folder = gc.createFolder(
+                parent_folder,
+                folder_name,
+                parentType="folder"
+              )
+        else:
+            me = gc.get("user/me")
+            new_folder = gc.createFolder(
+                me["_id"],
+                folder_name,
+                parentType="user"
+              )
+    except girder_client.HttpError as e:
+        if 'name already exists' in e.responseText:
+            click.echo(
+                "Folder already exists chose unique name."
+              )
+    return new_folder
+
+
+@click.group()
+def ascent():
+    """A cli to interact with the DIVE API """
+    pass
+
+
+@ascent.group()
+def upload():
+    pass
+
+
+@upload.command()
+@upload_arguments
+@global_options
+@click.option(
+    "--annotations-included",
+    is_flag=True,
+    help="Annotations for the image set are in the same directory and should be uploaded"
+)
+@upload_options
+def image_sequence(
+    parent_folder_id,
+    folder_name,
+    path: Path,
+    url,
+    port,
+    annotations_included,
+    annotations_path: Path
+):
+    """
+    Create folder with FOLDER_NAME in PARENT_FOLDER and upload a set of images from PATH\n
+
+    FOLDER_NAME is a unique name for the folder to be created \n
+    PATH is the the local path for the images to be uploaded
+    """
+    apiURL = url if url else "localhost"
+    local_port = port if port else 8010
+    gc = login(apiURL, local_port)
+    new_folder = create_folder(parent_folder_id, folder_name, gc)
+
+    if new_folder:
+        count = 1
+        images = len(list(path.iterdir()))
+        for file in path.iterdir():
+            if file.is_file():
+                if annotations_included:
+                    if file.suffix == '.json' or file.suffix == '.csv':
+                        images = images - 1
+                        gc.uploadFileToFolder(new_folder["_id"], file)
+                mimetype = mimetypes.guess_type(file.name)
+                if mimetype[0] in supportedImageTypes:
+                    click.echo(f"Uploading image {count} of {images}")
+                    gc.uploadFileToFolder(new_folder["_id"], file)
+                    count = count + 1
+
+        if annotations_path:
+            gc.uploadFileToFolder(new_folder["_id"], annotations_path)
+        gc.addMetadataToFolder(
+            new_folder["_id"],
+            {
+                "type": "image-sequence",
+                "fps": 1,
+            },
+        )
+        click.echo("Processing")
+        gc.sendRestRequest(
+            "POST",
+            f"dive_rpc/postprocess/{new_folder['_id']}",
+            data={"skipTranscoding": True},
+        )
+        click.echo(
+            f"Dataset ready at: http://{apiURL}:{local_port}/#/viewer/{new_folder['_id']}"
+            )
+
+
+@upload.command()
+@upload_arguments
+@upload_options
+def video(parent_folder, folder_name, path, url, port, annotations_path: Path):
+    """
+    Create folder with FOLDER_NAME in PARENT_FOLDER and upload a video from PATH\n
+
+    FOLDER_NAME is a unique name for the folder to be created \n
+    PATH is the the local path for the video to be uploaded
+    """
+    apiURL = url if url else "localhost"
+    local_port = port if port else 8010
+    gc = login(apiURL, local_port)
+    new_folder = create_folder(parent_folder, folder_name, gc)
+    if new_folder:
+        click.echo("Uploading video.")
+        gc.uploadFileToFolder(new_folder["_id"], path)
+        if annotations_path:
+            gc.uploadFileToFolder(new_folder["_id"], annotations_path)
+        gc.addMetadataToFolder(
+            new_folder["_id"],
+            {
+                "type": "video",
+                "fps": -1,
+            },
+        )
+        click.echo("Processing")
+        gc.sendRestRequest(
+            "POST",
+            f"dive_rpc/postprocess/{new_folder['_id']}",
+            data={"skipTranscoding": True},
+        )
+        click.echo(
+            f"Dataset ready at: http://{apiURL}:{local_port}/#/viewer/{new_folder['_id']}"
+        )
+
+
+@upload.command()
+@upload_arguments
+@upload_options
+def zip(parent_folder, folder_name, path, url, port, annotations_path: Path):
+    """
+    Create folder with FOLDER_NAME in PARENT_FOLDER and upload a zip file from PATH\n
+
+    FOLDER_NAME is a unique name for the folder to be created \n
+    PATH is the the local path for the zip file to be uploaded
+    """
+    apiURL = url if url else "localhost"
+    local_port = port if port else 8010
+    gc = login(apiURL, local_port)
+    new_folder = create_folder(parent_folder, folder_name, gc)
+    if new_folder:
+        gc.uploadFileToFolder(new_folder["_id"], path)
+        if annotations_path:
+            gc.uploadFileToFolder(new_folder["_id"], annotations_path)
+        click.echo(
+            f"Dataset ready at: http://{apiURL}:{local_port}/#/viewer/{new_folder['_id']}"
+        )
+# TODO unzip

ascent/setup.py

@@ -0,0 +1,13 @@
+from setuptools import setup
+
+setup(
+    name='ascent',
+    version='0.1.0',
+    py_modules=['ascent'],
+    install_requires=['click', 'pathlib', 'girder_client'],
+    entry_points={
+        'console_scripts': [
+            'ascent = ascent.cli:ascent'
+        ]
+    }
+)