488 lines
16 KiB
Python
488 lines
16 KiB
Python
from openflexure_microscope.api.utilities import gen, get_bool, JsonPayload
|
|
from openflexure_microscope.api.v1.views import MicroscopeView
|
|
from openflexure_microscope.utilities import filter_dict
|
|
|
|
from flask import Response, jsonify, request, abort, url_for, redirect, send_file
|
|
|
|
|
|
class ListAPI(MicroscopeView):
|
|
|
|
def get(self):
|
|
"""
|
|
Get list of image captures.
|
|
|
|
.. :quickref: Captures; Get collection of captures
|
|
|
|
:>header Accept: application/json
|
|
:query include_unavailable: return json representations of captures that have been completely deleted
|
|
|
|
:>jsonarr boolean available: availability of capture data
|
|
:>jsonarr string filename: filename of capture
|
|
:>jsonarr string id: unique id of the capture object
|
|
:>jsonarr boolean keep_on_disk: keep the capture file on microscope after closing
|
|
:>jsonarr boolean locked: file locked for modifications (mostly used for video recording)
|
|
:>jsonarr string path: path on pi storage to the capture file, if available
|
|
:>jsonarr boolean stream: capture stored in-memory as a BytesIO stream
|
|
:>jsonarr json uri: - **download** *(string)*: api uri to the capture file download
|
|
- **state** *(string)*: api uri to the capture json representation
|
|
|
|
:>header Content-Type: application/json
|
|
:status 200: capture found
|
|
:status 404: no capture found with that id
|
|
"""
|
|
include_unavailable = get_bool(request.args.get('include_unavailable'))
|
|
|
|
if include_unavailable:
|
|
captures = [image.state for image in self.microscope.camera.images]
|
|
else:
|
|
captures = [image.state for image in self.microscope.camera.images if image.state['available']]
|
|
|
|
return jsonify(captures)
|
|
|
|
def delete(self):
|
|
"""
|
|
Delete all captures (not yet implemented)
|
|
|
|
.. :quickref: Captures; Delete all captures
|
|
"""
|
|
for image in self.microscope.camera.images:
|
|
image.delete()
|
|
|
|
captures = [image.state for image in self.microscope.camera.images]
|
|
|
|
return jsonify(captures)
|
|
|
|
def post(self):
|
|
"""
|
|
Create a new image capture.
|
|
|
|
.. :quickref: Captures; New capture
|
|
|
|
**Example request**:
|
|
|
|
.. sourcecode:: http
|
|
|
|
POST /camera/capture HTTP/1.1
|
|
Accept: application/json
|
|
|
|
{
|
|
"filename": "myfirstcapture",
|
|
"temporary": false,
|
|
"use_video_port": true,
|
|
"bayer": true,
|
|
"size": {
|
|
"width": 640,
|
|
"height": 480
|
|
}
|
|
}
|
|
|
|
:>header Accept: application/json
|
|
|
|
:<json string filename: filename of stored capture
|
|
:<json boolean temporary: delete the capture file on microscope after closing
|
|
:<json boolean use_video_port: capture still image from the video port
|
|
:<json boolean bayer: keep raw capture data in the image file
|
|
:<json json size: - **x** *(int)*: x-axis resize
|
|
- **y** *(int)*: y-axis resize
|
|
|
|
:>json boolean available: availability of capture data
|
|
:>json string filename: filename of capture
|
|
:>json string id: unique id of the capture object
|
|
:>json boolean temporary: delete the capture file on microscope after closing
|
|
:>json boolean locked: file locked for modifications (mostly used for video recording)
|
|
:>json string path: path on pi storage to the capture file, if available
|
|
:>json boolean stream: capture stored in-memory as a BytesIO stream
|
|
:>json json uri: - **download** *(string)*: api uri to the capture file download
|
|
- **state** *(string)*: api uri to the capture json representation
|
|
|
|
:<header Content-Type: application/json
|
|
:status 200: capture created
|
|
"""
|
|
payload = JsonPayload(request)
|
|
|
|
filename = payload.param('filename')
|
|
temporary = payload.param('temporary', default=True, convert=bool)
|
|
use_video_port = payload.param('use_video_port', default=False, convert=bool)
|
|
bayer = payload.param('bayer', default=True, convert=bool)
|
|
metadata = payload.param('metadata', default={}, convert=dict)
|
|
tags = payload.param('tags', default=[], convert=list)
|
|
|
|
resize = payload.param('size', default=None)
|
|
if resize:
|
|
if ('width' in resize) and ('height' in resize):
|
|
resize = (int(resize['width']), int(resize['height'])) # Convert dict to tuple
|
|
else:
|
|
abort(404)
|
|
|
|
# Explicitally acquire lock (prevents empty files being created if lock is unavailable)
|
|
with self.microscope.camera.lock:
|
|
output = self.microscope.camera.new_image(
|
|
write_to_file=True,
|
|
temporary=temporary,
|
|
filename=filename)
|
|
|
|
self.microscope.camera.capture(
|
|
output,
|
|
use_video_port=use_video_port,
|
|
resize=resize,
|
|
bayer=bayer)
|
|
|
|
metadata.update({'Position': self.microscope.state['stage']['position']})
|
|
|
|
output.put_metadata(metadata)
|
|
output.put_tags(tags)
|
|
|
|
return jsonify(output.state)
|
|
|
|
|
|
class CaptureAPI(MicroscopeView):
|
|
|
|
def get(self, capture_id):
|
|
"""
|
|
Get JSON representation of a capture
|
|
|
|
.. :quickref: Capture; Get capture
|
|
|
|
**Example request**:
|
|
|
|
.. sourcecode:: http
|
|
|
|
GET /camera/capture/d0b2067abbb946f19351e075c5e7cd5b/ HTTP/1.1
|
|
Accept: application/json
|
|
|
|
**Example response**:
|
|
|
|
.. sourcecode:: http
|
|
|
|
HTTP/1.1 200 OK
|
|
Vary: Accept
|
|
Content-Type: application/json
|
|
|
|
{
|
|
"available": true,
|
|
"bytestream": false,
|
|
"keep_on_disk": false,
|
|
"locked": false,
|
|
"metadata": {
|
|
"filename": "2018-11-16_10-21-53.jpeg",
|
|
"id": "d0b2067abbb946f19351e075c5e7cd5b",
|
|
"path": "capture/2018-11-16_10-21-53.jpeg",
|
|
"time": "2018-11-16_10-21-53"
|
|
}
|
|
"uri": {
|
|
"download": "/api/v1/capture/d0b2067abbb946f19351e075c5e7cd5b/download",
|
|
"state": "/api/v1/capture/d0b2067abbb946f19351e075c5e7cd5b/"
|
|
}
|
|
}
|
|
|
|
:>json boolean available: availability of capture data
|
|
:>json string filename: filename of capture
|
|
:>json string id: unique id of the capture object
|
|
:>json boolean keep_on_disk: keep the capture file on microscope after closing
|
|
:>json boolean locked: file locked for modifications (mostly used for video recording)
|
|
:>json string path: path on pi storage to the capture file, if available
|
|
:>json boolean stream: capture stored in-memory as a BytesIO stream
|
|
:>json json uri: - **download** *(string)*: api uri to the capture file download
|
|
- **state** *(string)*: api uri to the capture json representation
|
|
|
|
"""
|
|
capture_obj = self.microscope.camera.image_from_id(capture_id)
|
|
|
|
if not capture_obj:
|
|
return abort(404) # 404 Not Found
|
|
|
|
# Get capture state
|
|
capture_metadata = capture_obj.state
|
|
|
|
# Add API routes to returned state
|
|
uri_dict = {
|
|
'uri': {'state': '{}'.format(url_for('.capture', capture_id=capture_obj.id))}
|
|
}
|
|
|
|
# If available, also add download link
|
|
if capture_metadata['available']:
|
|
uri_dict['uri']['download'] = '{}download/{}'.format(url_for('.capture', capture_id=capture_obj.id), capture_obj.filename)
|
|
|
|
capture_metadata.update(uri_dict)
|
|
|
|
return jsonify(capture_metadata)
|
|
|
|
def delete(self, capture_id):
|
|
"""
|
|
Delete all capture data from the Pi, even if `keep_on_disk=true;`.
|
|
|
|
.. :quickref: Capture; Delete capture.
|
|
"""
|
|
capture_obj = self.microscope.camera.image_from_id(capture_id)
|
|
|
|
if not capture_obj:
|
|
return abort(404) # 404 Not Found
|
|
|
|
capture_obj.delete()
|
|
|
|
return jsonify({"return": capture_id})
|
|
|
|
def put(self, capture_id):
|
|
"""
|
|
Add arbitrary metadata to the capture (stored in an accompanying capture `.yaml` file)
|
|
|
|
.. :quickref: Capture; Update capture metadata
|
|
|
|
**Example request**:
|
|
|
|
.. sourcecode:: http
|
|
|
|
PUT /camera/capture/d0b2067abbb946f19351e075c5e7cd5b HTTP/1.1
|
|
Accept: application/json
|
|
|
|
{
|
|
"user_id": "ofm_1234",
|
|
"patient_number": 1452,
|
|
}
|
|
|
|
:>header Accept: application/json
|
|
|
|
:<header Content-Type: application/json
|
|
:status 200: metadata updated
|
|
"""
|
|
|
|
capture_obj = self.microscope.camera.image_from_id(capture_id)
|
|
|
|
if not capture_obj:
|
|
return abort(404) # 404 Not Found
|
|
|
|
data_dict = JsonPayload(request).json
|
|
|
|
capture_obj.put_metadata(data_dict)
|
|
|
|
capture_metadata = capture_obj.state
|
|
|
|
return jsonify(capture_metadata)
|
|
|
|
|
|
class DownloadRedirectAPI(MicroscopeView):
|
|
def get(self, capture_id):
|
|
"""
|
|
Return image data for a capture.
|
|
|
|
Return capture data as an image file with the requested filename.
|
|
I.e., `/(capture_id)/download/foo.jpeg` will download the image as
|
|
`foo.jpeg`, regardless of the capture's initially set filename.
|
|
|
|
Route automatically redirects to download the capture under it's currently set filename.
|
|
I.e., `/(capture_id)/download` will
|
|
redirect to `/(capture_id)/download/(filename)`.
|
|
|
|
.. :quickref: Capture; Download capture image
|
|
|
|
**Example request**:
|
|
|
|
.. sourcecode:: http
|
|
|
|
GET /camera/capture/d0b2067abbb946f19351e075c5e7cd5b/download/2018-11-20_16-04-17.jpeg HTTP/1.1
|
|
Accept: image/jpeg
|
|
|
|
:>header Accept: image/jpeg
|
|
:query thumbnail: return an image thumbnail e.g. ?thumbnail=true
|
|
|
|
:>header Content-Type: image/jpeg
|
|
:status 200: capture data found
|
|
:status 404: no capture found with that id
|
|
|
|
"""
|
|
capture_obj = self.microscope.camera.image_from_id(capture_id)
|
|
|
|
if not capture_obj or not capture_obj.state['available']:
|
|
return abort(404) # 404 Not Found
|
|
|
|
thumbnail = get_bool(request.args.get('thumbnail'))
|
|
|
|
return redirect(url_for('.capture_download', capture_id=capture_id, filename=capture_obj.filename, thumbnail=thumbnail), code=307)
|
|
|
|
|
|
class DownloadAPI(MicroscopeView):
|
|
def get(self, capture_id, filename):
|
|
|
|
capture_obj = self.microscope.camera.image_from_id(capture_id)
|
|
|
|
if not capture_obj or not capture_obj.state['available']:
|
|
return abort(404) # 404 Not Found
|
|
|
|
thumbnail = get_bool(request.args.get('thumbnail'))
|
|
|
|
# If no filename is specified, redirect to the capture's currently set filename
|
|
if not filename:
|
|
return redirect(url_for('capture_download', capture_id=capture_id, filename=capture_obj.filename, thumbnail=thumbnail), code=307)
|
|
|
|
# Download the image data using the requested filename
|
|
if thumbnail:
|
|
img = capture_obj.thumbnail
|
|
else:
|
|
img = capture_obj.data
|
|
|
|
return send_file(
|
|
img,
|
|
mimetype='image/jpeg')
|
|
|
|
|
|
class MetadataRedirectAPI(MicroscopeView):
|
|
def get(self, capture_id):
|
|
"""
|
|
Return metadatadata for a capture.
|
|
|
|
Return capture metadata as a YAML file with the requested filename.
|
|
I.e., `/(capture_id)/download/bar.yaml` will download the file as
|
|
`bar.yaml`, regardless of the capture's initially set filename.
|
|
|
|
Route automatically redirects to download the capture metadata under it's currently set filename.
|
|
I.e., `/(capture_id)/download` will
|
|
redirect to `/(capture_id)/download/(filename)`.
|
|
|
|
.. :quickref: Capture; Download capture metadata
|
|
|
|
**Example request**:
|
|
|
|
.. sourcecode:: http
|
|
|
|
GET /camera/capture/d0b2067abbb946f19351e075c5e7cd5b/metadata/2018-11-20_16-04-17.yaml HTTP/1.1
|
|
Accept: text/yaml
|
|
|
|
:>header Accept: text/yaml
|
|
:query as_attachment: return the image as an attachment download e.g. ?as_attachment=true
|
|
|
|
:>header Content-Type: text/yaml
|
|
:status 200: capture data found
|
|
:status 404: no capture found with that id
|
|
|
|
"""
|
|
capture_obj = self.microscope.camera.image_from_id(capture_id)
|
|
|
|
if not capture_obj or not capture_obj.state['available']:
|
|
return abort(404) # 404 Not Found
|
|
|
|
return redirect(url_for('.metadata_download', capture_id=capture_id, filename=capture_obj.metadataname), code=307)
|
|
|
|
|
|
class MetadataAPI(MicroscopeView):
|
|
def get(self, capture_id, filename):
|
|
|
|
capture_obj = self.microscope.camera.image_from_id(capture_id)
|
|
|
|
if not capture_obj or not capture_obj.state['available']:
|
|
return abort(404) # 404 Not Found
|
|
|
|
# If no filename is specified, redirect to the capture's currently set filename
|
|
if not filename:
|
|
return redirect(url_for('capture_download', capture_id=capture_id, filename=capture_obj.metadataname), code=307)
|
|
|
|
# Download the metadata using the requested filename
|
|
data = capture_obj.yaml
|
|
|
|
return Response(
|
|
data,
|
|
mimetype="text/yaml")
|
|
|
|
|
|
class TagsAPI(MicroscopeView):
|
|
def get(self, capture_id):
|
|
"""
|
|
Return tag list for a capture.
|
|
|
|
.. :quickref: Capture; Show capture tags
|
|
|
|
**Example request**:
|
|
|
|
.. sourcecode:: http
|
|
|
|
GET /camera/capture/d0b2067abbb946f19351e075c5e7cd5b/tags HTTP/1.1
|
|
Accept: text/yaml
|
|
|
|
:>header Accept: text/yaml
|
|
|
|
:>header Content-Type: text/yaml
|
|
:status 200: capture data found
|
|
:status 404: no capture found with that id
|
|
"""
|
|
capture_obj = self.microscope.camera.image_from_id(capture_id)
|
|
|
|
if not capture_obj or not capture_obj.state['available']:
|
|
return abort(404) # 404 Not Found
|
|
|
|
metadata_tags = filter_dict(capture_obj.state, ['metadata', 'tags'])
|
|
|
|
return jsonify(metadata_tags)
|
|
|
|
def put(self, capture_id):
|
|
"""
|
|
Add tags to the capture
|
|
|
|
.. :quickref: Capture; Update capture tags
|
|
|
|
**Example request**:
|
|
|
|
.. sourcecode:: http
|
|
|
|
PUT /camera/capture/d0b2067abbb946f19351e075c5e7cd5b/tags HTTP/1.1
|
|
Accept: application/json
|
|
|
|
["tests", "mytag", "someothertag"]
|
|
|
|
:>header Accept: application/json
|
|
|
|
:<header Content-Type: application/json
|
|
:status 200: metadata updated
|
|
"""
|
|
|
|
capture_obj = self.microscope.camera.image_from_id(capture_id)
|
|
|
|
if not capture_obj or not capture_obj.state['available']:
|
|
return abort(404) # 404 Not Found
|
|
|
|
data_dict = JsonPayload(request).json
|
|
|
|
if type(data_dict) != list:
|
|
return abort(400)
|
|
|
|
for tag in data_dict:
|
|
capture_obj.put_tag(str(tag))
|
|
|
|
metadata_tags = filter_dict(capture_obj.state, ['metadata', 'tags'])
|
|
|
|
return jsonify(metadata_tags)
|
|
|
|
def delete(self, capture_id):
|
|
"""
|
|
Delete tags from the capture
|
|
|
|
.. :quickref: Capture; Delete tags.
|
|
|
|
**Example request**:
|
|
|
|
.. sourcecode:: http
|
|
|
|
DELETE /camera/capture/d0b2067abbb946f19351e075c5e7cd5b/tags HTTP/1.1
|
|
Accept: application/json
|
|
|
|
["tests", "mytag"]
|
|
|
|
:>header Accept: application/json
|
|
|
|
:<header Content-Type: application/json
|
|
:status 200: metadata updated
|
|
"""
|
|
capture_obj = self.microscope.camera.image_from_id(capture_id)
|
|
|
|
if not capture_obj:
|
|
return abort(404) # 404 Not Found
|
|
|
|
data_dict = JsonPayload(request).json
|
|
|
|
if type(data_dict) != list:
|
|
return abort(400)
|
|
|
|
for tag in data_dict:
|
|
capture_obj.delete_tag(str(tag))
|
|
|
|
metadata_tags = filter_dict(capture_obj.state, ['metadata', 'tags'])
|
|
|
|
return jsonify(metadata_tags)
|