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This commit is contained in:
Joel Collins 2019-09-15 14:17:52 +01:00
parent e213647217
commit 5966ce29be
57 changed files with 1938 additions and 1414 deletions
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63
openflexure_microscope/api/v1/blueprints/camera/__init__.py
View file

@ -7,51 +7,70 @@ from . import capture, record, preview, function
def construct_blueprint(microscope_obj):
blueprint = Blueprint('camera_blueprint', __name__)
blueprint = Blueprint("camera_blueprint", __name__)
# Metadata routes
blueprint.add_url_rule(
'/capture/<capture_id>/metadata/<filename>',
view_func=capture.MetadataAPI.as_view('metadata_download', microscope=microscope_obj))
"/capture/<capture_id>/metadata/<filename>",
view_func=capture.MetadataAPI.as_view(
"metadata_download", microscope=microscope_obj
),
)
blueprint.add_url_rule(
'/capture/<capture_id>/metadata',
view_func=capture.MetadataRedirectAPI.as_view('metadata_download_redirect', microscope=microscope_obj))
"/capture/<capture_id>/metadata",
view_func=capture.MetadataRedirectAPI.as_view(
"metadata_download_redirect", microscope=microscope_obj
),
)
# Tag routes
blueprint.add_url_rule(
'/capture/<capture_id>/tags',
view_func=capture.TagsAPI.as_view('capture_tags', microscope=microscope_obj))
"/capture/<capture_id>/tags",
view_func=capture.TagsAPI.as_view("capture_tags", microscope=microscope_obj),
)
# Capture routes
blueprint.add_url_rule(
'/capture/<capture_id>/download/<filename>',
view_func=capture.DownloadAPI.as_view('capture_download', microscope=microscope_obj))
"/capture/<capture_id>/download/<filename>",
view_func=capture.DownloadAPI.as_view(
"capture_download", microscope=microscope_obj
),
)
blueprint.add_url_rule(
'/capture/<capture_id>/download',
view_func=capture.DownloadRedirectAPI.as_view('capture_download_redirect', microscope=microscope_obj))
"/capture/<capture_id>/download",
view_func=capture.DownloadRedirectAPI.as_view(
"capture_download_redirect", microscope=microscope_obj
),
)
blueprint.add_url_rule(
'/capture/<capture_id>/',
view_func=capture.CaptureAPI.as_view('capture', microscope=microscope_obj))
"/capture/<capture_id>/",
view_func=capture.CaptureAPI.as_view("capture", microscope=microscope_obj),
)
blueprint.add_url_rule(
'/capture/',
view_func=capture.ListAPI.as_view('capture_list', microscope=microscope_obj))
"/capture/",
view_func=capture.ListAPI.as_view("capture_list", microscope=microscope_obj),
)
# Preview routes
blueprint.add_url_rule(
'/preview/<string:operation>',
view_func=preview.GPUPreviewAPI.as_view('gpu_preview', microscope=microscope_obj))
"/preview/<string:operation>",
view_func=preview.GPUPreviewAPI.as_view(
"gpu_preview", microscope=microscope_obj
),
)
# Function routes
blueprint.add_url_rule(
'/overlay',
view_func=function.OverlayAPI.as_view('overlay', microscope=microscope_obj))
"/overlay",
view_func=function.OverlayAPI.as_view("overlay", microscope=microscope_obj),
)
blueprint.add_url_rule(
'/zoom',
view_func=function.ZoomAPI.as_view('zoom', microscope=microscope_obj))
"/zoom", view_func=function.ZoomAPI.as_view("zoom", microscope=microscope_obj)
)
return(blueprint)
return blueprint

157
openflexure_microscope/api/v1/blueprints/camera/capture.py
View file

@ -6,7 +6,6 @@ from flask import Response, jsonify, request, abort, url_for, redirect, send_fil
class ListAPI(MicroscopeView):
def get(self):
"""
Get list of image captures.
@ -30,12 +29,16 @@ class ListAPI(MicroscopeView):
:status 200: capture found
:status 404: no capture found with that id
"""
include_unavailable = get_bool(request.args.get('include_unavailable'))
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']]
captures = [
image.state
for image in self.microscope.camera.images
if image.state["available"]
]
return jsonify(captures)
@ -100,38 +103,40 @@ class ListAPI(MicroscopeView):
"""
payload = JsonResponse(request)
filename = payload.param('filename')
temporary = payload.param('temporary', default=False, 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)
filename = payload.param("filename")
temporary = payload.param("temporary", default=False, 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)
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
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)
write_to_file=True, temporary=temporary, filename=filename
)
self.microscope.camera.capture(
output,
use_video_port=use_video_port,
resize=resize,
bayer=bayer)
output, use_video_port=use_video_port, resize=resize, bayer=bayer
)
metadata.update({
'position': self.microscope.state['stage']['position'],
'microscope_id': self.microscope.id,
'microscope_name': self.microscope.name
})
metadata.update(
{
"position": self.microscope.state["stage"]["position"],
"microscope_id": self.microscope.id,
"microscope_name": self.microscope.name,
}
)
output.put_metadata(metadata)
output.put_tags(tags)
@ -140,7 +145,6 @@ class ListAPI(MicroscopeView):
class CaptureAPI(MicroscopeView):
def get(self, capture_id):
"""
Get JSON representation of a capture
@ -200,14 +204,15 @@ class CaptureAPI(MicroscopeView):
# Add API routes to returned state
uri_dict = {
'uri': {'state': '{}'.format(url_for('.capture', capture_id=capture_obj.id))}
"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
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)
@ -257,7 +262,7 @@ class CaptureAPI(MicroscopeView):
if not capture_obj:
return abort(404) # 404 Not Found
data_dict = JsonResponse(request).json
capture_obj.put_metadata(data_dict)
@ -299,17 +304,20 @@ class DownloadRedirectAPI(MicroscopeView):
"""
capture_obj = self.microscope.camera.image_from_id(capture_id)
if not capture_obj or not capture_obj.state['available']:
if not capture_obj or not capture_obj.state["available"]:
return abort(404) # 404 Not Found
thumbnail = get_bool(request.args.get('thumbnail'))
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)
return redirect(
url_for(
".capture_download",
capture_id=capture_id,
filename=capture_obj.filename,
thumbnail=thumbnail,
),
code=307,
)
class DownloadAPI(MicroscopeView):
@ -317,19 +325,22 @@ class DownloadAPI(MicroscopeView):
capture_obj = self.microscope.camera.image_from_id(capture_id)
if not capture_obj or not capture_obj.state['available']:
if not capture_obj or not capture_obj.state["available"]:
return abort(404) # 404 Not Found
thumbnail = get_bool(request.args.get('thumbnail'))
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)
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:
@ -337,9 +348,7 @@ class DownloadAPI(MicroscopeView):
else:
img = capture_obj.data
return send_file(
img,
mimetype='image/jpeg')
return send_file(img, mimetype="image/jpeg")
class MetadataRedirectAPI(MicroscopeView):
@ -374,14 +383,17 @@ class MetadataRedirectAPI(MicroscopeView):
"""
capture_obj = self.microscope.camera.image_from_id(capture_id)
if not capture_obj or not capture_obj.state['available']:
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)
return redirect(
url_for(
".metadata_download",
capture_id=capture_id,
filename=capture_obj.metadataname,
),
code=307,
)
class MetadataAPI(MicroscopeView):
@ -389,23 +401,24 @@ class MetadataAPI(MicroscopeView):
capture_obj = self.microscope.camera.image_from_id(capture_id)
if not capture_obj or not capture_obj.state['available']:
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)
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")
return Response(data, mimetype="text/yaml")
class TagsAPI(MicroscopeView):
@ -430,13 +443,13 @@ class TagsAPI(MicroscopeView):
"""
capture_obj = self.microscope.camera.image_from_id(capture_id)
if not capture_obj or not capture_obj.state['available']:
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'])
metadata_tags = filter_dict(capture_obj.state, ["metadata", "tags"])
return jsonify(metadata_tags)
def put(self, capture_id):
"""
Add tags to the capture
@ -460,9 +473,9 @@ class TagsAPI(MicroscopeView):
capture_obj = self.microscope.camera.image_from_id(capture_id)
if not capture_obj or not capture_obj.state['available']:
if not capture_obj or not capture_obj.state["available"]:
return abort(404) # 404 Not Found
data_dict = JsonResponse(request).json
if type(data_dict) != list:
@ -470,7 +483,7 @@ class TagsAPI(MicroscopeView):
capture_obj.put_tags(data_dict)
metadata_tags = filter_dict(capture_obj.state, ['metadata', 'tags'])
metadata_tags = filter_dict(capture_obj.state, ["metadata", "tags"])
return jsonify(metadata_tags)
@ -507,6 +520,6 @@ class TagsAPI(MicroscopeView):
for tag in data_dict:
capture_obj.delete_tag(str(tag))
metadata_tags = filter_dict(capture_obj.state, ['metadata', 'tags'])
metadata_tags = filter_dict(capture_obj.state, ["metadata", "tags"])
return jsonify(metadata_tags)

16
openflexure_microscope/api/v1/blueprints/camera/function.py
View file

@ -5,7 +5,6 @@ from flask import jsonify, request
class ZoomAPI(MicroscopeView):
def get(self):
"""
Get the current zoom value
@ -17,9 +16,9 @@ class ZoomAPI(MicroscopeView):
:<header Content-Type: application/json
:status 200: preview started/stopped
"""
zoom_value = self.microscope.camera.state['zoom_value']
zoom_value = self.microscope.camera.state["zoom_value"]
return jsonify({'zoom_value': zoom_value})
return jsonify({"zoom_value": zoom_value})
def post(self):
"""
@ -44,7 +43,7 @@ class ZoomAPI(MicroscopeView):
:status 200: preview started/stopped
"""
payload = JsonResponse(request)
zoom_value = payload.param('zoom_value', default=1.0, convert=float)
zoom_value = payload.param("zoom_value", default=1.0, convert=float)
self.microscope.camera.set_zoom(zoom_value)
@ -52,7 +51,6 @@ class ZoomAPI(MicroscopeView):
class OverlayAPI(MicroscopeView):
def get(self):
"""
Get overlay text
@ -67,7 +65,7 @@ class OverlayAPI(MicroscopeView):
text = self.microscope.camera.camera.annotate_text
size = self.microscope.camera.camera.annotate_text_size
return jsonify({'text': text, 'size': size})
return jsonify({"text": text, "size": size})
def post(self):
"""
@ -94,10 +92,10 @@ class OverlayAPI(MicroscopeView):
"""
payload = JsonResponse(request)
text = payload.param('text', default="", convert=str)
size = payload.param('size', default=50, convert=int)
text = payload.param("text", default="", convert=str)
size = payload.param("size", default=50, convert=int)
self.microscope.camera.camera.annotate_text = text
self.microscope.camera.camera.annotate_text_size = size
return jsonify({'text': text, 'size': size})
return jsonify({"text": text, "size": size})

3
openflexure_microscope/api/v1/blueprints/camera/preview.py
View file

@ -6,7 +6,6 @@ import logging
class GPUPreviewAPI(MicroscopeView):
def post(self, operation):
"""
Start or stop the onboard GPU preview.
@ -39,7 +38,7 @@ class GPUPreviewAPI(MicroscopeView):
if operation == "start":
payload = JsonResponse(request)
window = payload.param('window', default=[])
window = payload.param("window", default=[])
logging.debug(window)
if len(window) != 4: