[Snapshots] - New snapshot routine

mxcubeweb/core/components/queue.py

@@ -1439,6 +1439,7 @@ def _create_dc(self):
         dc_model = qmo.DataCollection()
         dc_model.set_origin(ORIGIN_MX3)
         dc_model.center_before_collect = True
+        dc_model.take_snapshots = self.app.NUM_SNAPSHOTS
         dc_entry = qe.DataCollectionQueueEntry(Mock(), dc_model)
 
         return dc_model, dc_entry
@@ -2127,6 +2128,7 @@ def is_interleaved(self, node):
 
     def init_queue_settings(self):
         self.app.NUM_SNAPSHOTS = HWR.beamline.collect.get_property("num_snapshots", 4)
+        HWR.beamline.collect.number_of_snapshots = self.app.NUM_SNAPSHOTS
         self.app.AUTO_MOUNT_SAMPLE = HWR.beamline.collect.get_property(
             "auto_mount_sample", False
         )
@@ -2387,7 +2389,7 @@ def get_default_task_parameters(self, task_name):
                 "inverse_beam": False,
                 "take_dark_current": True,
                 "skip_existing_images": False,
-                "take_snapshots": True,
+                "take_snapshots": self.app.NUM_SNAPSHOTS,
                 "helical": False,
                 "mesh": False,
                 "prefixTemplate": "{PREFIX}_{POSITION}",

mxcubeweb/core/components/sampleview.py

@@ -1,17 +1,12 @@
 # -*- coding: utf-8 -*-
 import logging
-import types
-import sys
-import os
-import inspect
 
 import PIL
 import gevent.event
 
 from flask import Response
 
 from io import StringIO
-import base64
 
 from mxcubeweb.core.util.convertutils import to_camel, from_camel
 
@@ -118,12 +113,6 @@ def __init__(self, app, config):
         self._centring_point_id = None
         self.http_streamer = HttpStreamer()
 
-        enable_snapshots(
-            HWR.beamline.collect,
-            HWR.beamline.diffractometer,
-            HWR.beamline.sample_view,
-        )
-
         HWR.beamline.sample_view.connect("shapesChanged", self._emit_shapes_updated)
 
         zoom_motor = HWR.beamline.diffractometer.get_object_by_role("zoom")
@@ -509,109 +498,3 @@ def set_centring_method(self, method):
             self.app.CENTRING_METHOD = CENTRING_METHOD.MANUAL
 
         logging.getLogger("user_level_log").info(msg)
-
-
-def enable_snapshots(collect_object, diffractometer_object, sample_view):
-    def _snapshot_received(data):
-        snapshot_jpg = data.get("data", "")
-
-        global SNAPSHOT
-        SNAPSHOT = base64.b64decode(snapshot_jpg)
-        SNAPSHOT_RECEIVED.set()
-
-    def _do_take_snapshot(filename, bw=False):
-        sample_view.save_snapshot(filename, overlay=False, bw=bw)
-
-    def save_snapshot(self, filename, bw=False):
-        sample_view.save_snapshot(filename, overlay=False, bw=bw)
-        # _do_take_snapshot(filename, bw)
-
-    def take_snapshots(self, snapshots=None, _do_take_snapshot=_do_take_snapshot):
-        from mxcubeweb.app import MXCUBEApplication as mxcube
-
-        if snapshots is None:
-            # called via AbstractCollect
-            dc_params = self.current_dc_parameters
-            move_omega_relative = diffractometer_object.move_omega_relative
-        else:
-            # called via AbstractMultiCollect
-            # calling_frame = inspect.currentframe()
-            calling_frame = inspect.currentframe().f_back.f_back
-
-            dc_params = calling_frame.f_locals["data_collect_parameters"]
-            move_omega_relative = diffractometer_object.phiMotor.set_value_relative
-
-        if dc_params["take_snapshots"]:
-            # The below does not work. NUM_SNAPSHOTS needs to e got in somehow
-            number_of_snapshots = mxcube.NUM_SNAPSHOTS
-        else:
-            number_of_snapshots = 0
-
-        if number_of_snapshots > 0:
-            if (
-                hasattr(diffractometer_object, "set_phase")
-                and diffractometer_object.get_current_phase() != "Centring"
-            ):
-                use_custom_snapshot_routine = diffractometer_object.get_property(
-                    "custom_snapshot_script_dir", None
-                )
-                if not use_custom_snapshot_routine:
-                    logging.getLogger("user_level_log").info(
-                        "Moving Diffractometer to CentringPhase Not done for tests (DN)"
-                    )
-
-                    diffractometer_object.set_phase("Centring", wait=True, timeout=200)
-
-            snapshot_directory = dc_params["fileinfo"]["archive_directory"]
-            if not os.path.exists(snapshot_directory):
-                try:
-                    self.create_directories(snapshot_directory)
-                except Exception:
-                    logging.getLogger("MX3.HWR").exception(
-                        "Collection: Error creating snapshot directory"
-                    )
-
-            logging.getLogger("user_level_log").info(
-                "Taking %d sample snapshot(s)" % number_of_snapshots
-            )
-
-            for snapshot_index in range(number_of_snapshots):
-                snapshot_filename = os.path.join(
-                    snapshot_directory,
-                    "%s_%s_%s.snapshot.jpeg"
-                    % (
-                        dc_params["fileinfo"]["prefix"],
-                        dc_params["fileinfo"]["run_number"],
-                        (snapshot_index + 1),
-                    ),
-                )
-                dc_params[
-                    "xtalSnapshotFullPath%i" % (snapshot_index + 1)
-                ] = snapshot_filename
-
-                try:
-                    logging.getLogger("MX3.HWR").info(
-                        "Taking snapshot number: %d" % (snapshot_index + 1)
-                    )
-                    _do_take_snapshot(snapshot_filename)
-                    # diffractometer.save_snapshot(snapshot_filename)
-                except Exception as ex:
-                    sys.excepthook(*sys.exc_info())
-                    raise RuntimeError(
-                        "Could not take snapshot '%s'",
-                        snapshot_filename,
-                    ) from ex
-
-                if number_of_snapshots > 1:
-                    move_omega_relative(90)
-                    diffractometer_object.wait_ready()
-
-    collect_object.take_crystal_snapshots = types.MethodType(
-        take_snapshots, collect_object
-    )
-
-    diffractometer_object.save_snapshot = types.MethodType(
-        save_snapshot, diffractometer_object
-    )
-
-    sample_view.set_ui_snapshot_cb(save_snapshot)

mxcubeweb/core/components/user/usermanager.py

@@ -1,5 +1,4 @@
 import logging
-import json
 import uuid
 import datetime
 import requests
@@ -23,14 +22,13 @@
 class BaseUserManager(ComponentBase):
     def __init__(self, app, config):
         super().__init__(app, config)
-
         self.oauth_client = OAuth(app=app.server.flask)
-        self.oauth_issuer = "https://websso.esrf.fr/realms/ESRF/"
-        self.oauth_logout_url = (
-            "https://websso.esrf.fr/auth/realms/ESRF/protocol/openid-connect/logout"
-        )
-        self.oauth_client_secret = "95nOugpRxwF3ttXxYnXFiK6bou5wtSP1"
-        self.oauth_client_id = "mxcube"
+
+        self.oauth_issuer = self.app.CONFIG.sso.ISSUER
+        self.oauth_logout_url = self.app.CONFIG.sso.LOGOUT_URI
+        self.oauth_client_secret = self.app.CONFIG.sso.CLIENT_SECRET
+        self.oauth_client_id = self.app.CONFIG.sso.CLIENT_ID
+
         self.oauth_client.register(
             name="keycloak",
             client_id=self.oauth_client_id,

mxcubeweb/routes/queue.py

@@ -337,6 +337,7 @@ def set_autmount():
     def set_num_snapshots():
         data = request.get_json()
         app.NUM_SNAPSHOTS = data.get("numSnapshots", 4)
+        HWR.beamline.collect.number_of_snapshots = app.NUM_SNAPSHOTS
         resp = jsonify({"numSnapshots": data.get("numSnapshots", 4)})
         resp.status_code = 200
 

mxcubeweb/routes/samplecentring.py

@@ -1,7 +1,6 @@
-import os
 import json
 
-from flask import Blueprint, Response, jsonify, request
+from flask import Blueprint, Response, jsonify, request, send_file
 
 from mxcubecore import HardwareRepository as HWR
 
@@ -35,22 +34,29 @@ def unsubscribe_to_camera():
         HWR.beamline.sample_view.camera.streaming_greenlet.kill()
         return Response(status=200)
 
-    @bp.route("/camera/save", methods=["PUT"])
+    @bp.route("/camera/snapshot", methods=["POST"])
     @server.restrict
     def snapshot():
         """
-        Save snapshot of the sample view
-        data = {generic_data, "Path": path} # not sure if path should be available,
-        or directly use the user/proposal path
-        Return: 'True' if command issued succesfully, otherwise 'False'.
+        Take snapshot of the sample view
+        data = {"overlay": overlay_data} overlay is the image data to overlay on sample image,
+        it should normally contain the data of shapes drawn on canvas.
+        Return: Overlayed image uri, if successful, statuscode 500 otherwise.
         """
         try:
-            HWR.beamline.sample_view.camera.takeSnapshot(
-                os.path.join(os.path.dirname(__file__), "snapshots/")
+            overlay = json.loads(request.data).get("overlay")
+            snapshot_data_uri = HWR.beamline.sample_view.take_snapshot(
+                overlay_data=overlay,
             )
-            return "True"
-        except Exception:
-            return "False"
+            snapshot_data_uri.seek(0)
+            return send_file(
+                snapshot_data_uri,
+                mimetype="image/jpeg",
+                as_attachment=True,
+                download_name="test.png",
+            )
+        except Exception as e:
+            return jsonify({"error": str(e)}), 500
 
     @bp.route("/camera", methods=["GET"])
     @server.restrict

test/input_parameters.py

@@ -165,7 +165,7 @@
         "subDirTemplate": "{ACRONYM}/{ACRONYM}-{NAME}",
         "sub_wedge_size": 10,
         "take_dark_current": True,
-        "take_snapshots": True,
+        "take_snapshots": 4,
         "take_video": False,
         "transmission": 10,
     },
@@ -241,7 +241,7 @@
         "subDirTemplate": "{ACRONYM}/{ACRONYM}-{NAME}",
         "sub_wedge_size": 10,
         "take_dark_current": True,
-        "take_snapshots": True,
+        "take_snapshots": 4,
         "take_video": False,
         "transmission": 10,
         "use_aimed_multiplicity": False,
@@ -297,7 +297,7 @@
         "subDirTemplate": "{ACRONYM}/{ACRONYM}-{NAME}",
         "sub_wedge_size": 10,
         "take_dark_current": True,
-        "take_snapshots": True,
+        "take_snapshots": 4,
         "take_video": False,
         "transmission": 10,
     },
@@ -349,7 +349,7 @@
         "subDirTemplate": "{ACRONYM}/{ACRONYM}-{NAME}",
         "sub_wedge_size": 10,
         "take_dark_current": True,
-        "take_snapshots": True,
+        "take_snapshots": 4,
         "take_video": False,
         "transmission": 10,
     },

ui/src/api/sampleview.js

@@ -57,3 +57,7 @@ export function sendMoveToBeam(x, y) {
 export function sendUpdateMotorPosition(motorName, value) {
   return endpoint.put(undefined, `/${motorName}/${value}`).res();
 }
+
+export function sendTakeSnapshot(canvasData) {
+  return endpoint.post({ overlay: canvasData }, '/camera/snapshot').blob();
+}

ui/src/components/SampleView/SampleControls.jsx

@@ -8,9 +8,11 @@ import 'fabric';
 
 import OneAxisTranslationControl from '../MotorInput/OneAxisTranslationControl';
 import { MOTOR_STATE } from '../../constants';
+import { sendTakeSnapshot } from '../../api/sampleview';
 
 import { find } from 'lodash';
 import styles from './SampleControls.module.css';
+import { downloadImage } from './utils';
 
 const { fabric } = window;
 
@@ -19,7 +21,7 @@ export default class SampleControls extends React.Component {
     super(props);
 
     this.takeSnapShot = this.takeSnapShot.bind(this);
-    this.doTakeSnapshot = this.doTakeSnapshot.bind(this);
+    this.getCanvasData = this.getCanvasData.bind(this);
     this.toggleFrontLight = this.toggleLight.bind(
       this,
       'diffractometer.frontlight',
@@ -33,10 +35,6 @@ export default class SampleControls extends React.Component {
     this.availableVideoSizes = this.availableVideoSizes.bind(this);
   }
 
-  componentDidMount() {
-    window.takeSnapshot = this.doTakeSnapshot;
-  }
-
   toggleDrawGrid() {
     // Cancel click centering before draw grid is started
     if (this.props.currentSampleID === '') {
@@ -50,20 +48,24 @@ export default class SampleControls extends React.Component {
     }
   }
 
-  doTakeSnapshot() {
+  getCanvasData() {
     const img = document.querySelector('#sample-img');
     const fimg = new fabric.Image(img);
     fimg.scale(this.props.imageRatio);
     let imgDataURI = '';
     this.props.canvas.setBackgroundImage(fimg);
     this.props.canvas.renderAll();
-    imgDataURI = this.props.canvas.toDataURL({ format: 'jpeg' });
+    imgDataURI = this.props.canvas.toDataURL({
+      format: 'png',
+      backgroundColor: null,
+    });
     this.props.canvas.setBackgroundImage(0);
     this.props.canvas.renderAll();
-    return { data: imgDataURI.slice(23), mime: imgDataURI.slice(0, 23) };
+    // this function should only return the data not the mime
+    return imgDataURI.split(',')[1];
   }
 
-  takeSnapShot(evt) {
+  async takeSnapShot() {
     /* eslint-disable unicorn/consistent-function-scoping */
     function imageEpolog(props) {
       const { sampleID } = props.currentSampleID;
@@ -76,11 +78,10 @@ export default class SampleControls extends React.Component {
       return 'no-sample';
     }
 
-    const img = this.doTakeSnapshot();
+    const processedImgBlob = await sendTakeSnapshot(this.getCanvasData());
     const filename = `${this.props.proposal}-${imageEpolog(this.props)}.jpeg`;
 
-    evt.currentTarget.href = img.mime + img.data;
-    evt.currentTarget.download = filename;
+    downloadImage(processedImgBlob, filename);
   }
 
   toggleCentring() {
@@ -170,11 +171,7 @@ export default class SampleControls extends React.Component {
       <div className={styles.controls}>
         {this.props.getControlAvailability('snapshot') && (
           <Button
-            as="a"
             className={styles.controlBtn}
-            href="#"
-            target="_blank"
-            download
             title="Take snapshot"
             data-toggle="tooltip"
             onClick={this.takeSnapShot}

ui/src/components/SampleView/utils.js

@@ -0,0 +1,10 @@
+export function downloadImage(blob, download_name) {
+    const url = window.URL.createObjectURL(new Blob([blob]));
+    const link = document.createElement('a');
+    link.href = url;
+    link.setAttribute('download', download_name);
+    document.body.append(link);
+    link.click();
+    link.remove();
+    URL.revokeObjectURL(url);
+}