Merge pull request #2782 from pieleric/feature-support-hardware-synch…

…ronized-acquisition-on-sparc

[feature] Support hardware synchronized acquisition on SPARC

install/linux/usr/share/odemis/sim/sparc2-nidaq-sim.odm.yaml

@@ -27,8 +27,8 @@ SPARC2: {
         delay: { # Time it takes before a component is accessible
             "Calibration Light": 0, # To turn on/off the light, it's immediate
             "CL PMT control unit": 0,
-            "Camera": 3,
-            "Spectrograph": 5,
+            "Camera": 2,
+            "Spectrograph": 2,
             "Optical Actuators": 1
         },
         init: { # Which component to power on from the very beginning (to save time)
@@ -164,7 +164,6 @@ SPARC2: {
     },
 }
 
-# In reality, this is a Zyla, but you need libandor3-dev to simulate an AndorCam3
 # Depending exactly on the configuration, it might also be used for spectrometer
 "Camera": {
     class: andorcam2.AndorCam2,
@@ -179,7 +178,7 @@ SPARC2: {
 
 "Spectrometer Vis-NIR": {
     class: spectrometer.CompositedSpectrometer,
-    role: spectrometer-integrated,
+    role: spectrometer,
     dependencies: {detector: "Camera", spectrograph: "Spectrograph"},
     init: {
         transp: [1, -2], # only applied to the spectrometer data (not raw CCD)
@@ -279,7 +278,7 @@ SPARC2: {
         address: null,
         axes: ["l1", "l2", "cl-sel", "fw", "slit"],
         # These values are adapted to make the simulator roughly the same speed
-        ustepsize: [25.1e-9, 25.1e-9, 26.1e-9, 3.392e-5, 5.e-9], # m/µstep, excepted for the fw: rad/µstep
+        ustepsize: [25.1e-8, 25.1e-8, 26.1e-8, 3.392e-4, 5.e-8], # m/µstep, excepted for the fw: rad/µstep (adjusted for the simulator)
         unit: ["m", "m", "m", "rad", "m"],
         refproc: "Standard",
         refswitch: {"l1": 0, "l2": 0, "cl-sel": 4, "fw": 4},

plugins/cliccd.py

@@ -39,36 +39,35 @@ class SEMCLCCDStream(SEMCCDMDStream):
 
     def _preprocessData(self, n, data, i):
         """
-        return (int): mean of the data
+        return: mean of the data (if CCD)
         """
         # We only care about the CCD data
-        if n < len(self.streams) - 1:
-            return super(SEMCLCCDStream, self)._preprocessData(n, data, i)
-
-        # Computing the sum or the mean is theoretically equivalent, but the sum
-        # provides gigantic values while the mean gives values in the same order
-        # as in the original data. Note that we cannot use the original dtype
-        # because if it's an integer it will likely cause quantisation (as a
-        # large part of the image received is identical for all the e-beam
-        # positions scanned).
-        return data.mean()
-
-    def _assembleLiveData(self, n, raw_data, px_idx, rep, pol_idx):
+        if n == len(self.streams) - 1:
+            # Computing the sum or the mean is theoretically equivalent, but the sum
+            # provides gigantic values while the mean gives values in the same order
+            # as in the original data. Note that we cannot use the original dtype
+            # because if it's an integer it will likely cause quantisation (as a
+            # large part of the image received is identical for all the e-beam
+            # positions scanned).
+            data = data.mean()
+
+        return super()._preprocessData(n, data, i)
+
+    def _assembleLiveData(self, n, raw_data, px_idx, px_pos, rep, pol_idx=0):
         if n != self._ccd_idx:
-            return super(SEMCLCCDStream, self)._assembleLiveData(n, raw_data, px_idx, rep, pol_idx)
+            return super()._assembleLiveData(n, raw_data, px_idx, px_pos, rep, pol_idx)
 
         if pol_idx > len(self._live_data[n]) - 1:
             # New polarization => new DataArray
             md = raw_data.metadata.copy()
-            # Compute metadata based on SEM metadata
-            semmd = self._live_data[0][pol_idx].metadata
-            # handle sub-pixels (aka fuzzing)
-            md[MD_PIXEL_SIZE] = (semmd[MD_PIXEL_SIZE][0] * self._emitter.resolution.value[0],
-                                 semmd[MD_PIXEL_SIZE][1] * self._emitter.resolution.value[1])
-            md[MD_POS] = self._live_data[0][pol_idx].metadata[MD_POS]
-            md[MD_DIMS] = "YX"
-            md[MD_DESCRIPTION] = self._streams[n].name.value
-            # Make sure it doesn't contain metadata related to AR
+            # Compute metadata to match the SEM metadata
+            center, pxs = self._get_center_pxs(rep, (1, 1), self._pxs, px_pos)
+            md.update({MD_POS: center,
+                       MD_PIXEL_SIZE: pxs,
+                       MD_DIMS: "YX",
+                       MD_DESCRIPTION: self._streams[n].name.value})
+
+            # Remove any metadata related to AR & Spectrometry
             for k in (model.MD_AR_POLE, model.MD_AR_MIRROR_BOTTOM, model.MD_AR_MIRROR_TOP,
                       model.MD_AR_FOCUS_DISTANCE, model.MD_AR_HOLE_DIAMETER, model.MD_AR_PARABOLA_F,
                       model.MD_AR_XMAX, model.MD_ROTATION, model.MD_WL_LIST):
@@ -82,7 +81,7 @@ def _assembleLiveData(self, n, raw_data, px_idx, rep, pol_idx):
 
 class CLiCCDPlugin(Plugin):
     name = "CL intensity CCD"
-    __version__ = "1.2"
+    __version__ = "1.3"
     __author__ = u"Éric Piel"
     __license__ = "GPLv2"
 

plugins/secom_cl.py

@@ -538,7 +538,7 @@ def __init__(self, name, streams):
         """
         :param streams: ([Stream]) The streams to acquire.
         """
-        super(SECOMCLSEMMDStream, self).__init__(name, streams)
+        super().__init__(name, streams)
 
         self.filename = model.StringVA("a.tiff")
         self.firstOptImg = None  # save the first optical image for display in analysis tab
@@ -552,7 +552,7 @@ def _runAcquisition(self, future):
         """
         self.ccd_roi = sem_roi_to_ccd(self._emitter, self._ccd, self.roi.value, self._sccd.roi_margin.value)
 
-        return super(SECOMCLSEMMDStream, self)._runAcquisition(future)
+        return super()._runAcquisition(future)
 
     def _preprocessData(self, n, data, i):
         """
@@ -564,7 +564,7 @@ def _preprocessData(self, n, data, i):
         :returns: (value) The value as needed by _assembleFinalData.
         """
         if n != self._ccd_idx:
-            return super(SECOMCLSEMMDStream, self)._preprocessData(n, data, i)
+            return super()._preprocessData(n, data, i)
 
         ccd_roi = self.ccd_roi
         data = data[ccd_roi[1]: ccd_roi[3] + 1, ccd_roi[0]: ccd_roi[2] + 1]  # crop
@@ -596,9 +596,9 @@ def _preprocessData(self, n, data, i):
         # Return something, but not the data to avoid data being cached.
         return model.DataArray(numpy.array([0]))
 
-    def _assembleLiveData(self, n, raw_data, px_idx, rep, pol_idx):
+    def _assembleLiveData(self, n, raw_data, px_idx, px_pos, rep, pol_idx=0):
         if n != self._ccd_idx:
-            return super(SECOMCLSEMMDStream, self)._assembleLiveData(n, raw_data, px_idx, rep, pol_idx)
+            return super()._assembleLiveData(n, raw_data, px_idx, px_pos, rep, pol_idx)
 
         # For other streams (CL) don't do a live update
         return
@@ -610,7 +610,7 @@ def _assembleFinalData(self, n, data):
         :param raw_das: (list) List of data acquired for given detector n.
         """
         if n != self._ccd_idx:
-            super(SECOMCLSEMMDStream, self)._assembleFinalData(n, data)
+            super()._assembleFinalData(n, data)
 
         # For other streams (CL) don't do anything
         return
@@ -685,7 +685,7 @@ class CLAcqPlugin(Plugin):
     spots on the sample along a grid. Can also be used as a plugin.
     """
     name = "CL acquisition for SECOM"
-    __version__ = "2.0"
+    __version__ = "2.1"
     __author__ = u"Éric Piel, Lennard Voortman, Sabrina Rossberger"
     __license__ = "Public domain"
 

plugins/spectrum_arbscor.py

@@ -141,23 +141,25 @@ def _getSpotPositions(self):
         return pos
 
     def _assembleLiveData(self, n: int, raw_data: "DataArray",
-                          px_idx: Tuple[int, int], rep: Tuple[int, int], pol_idx: int):
+                          px_idx: Tuple[int, int], px_pos: Tuple[float, float],
+                          rep: Tuple[int, int], pol_idx: int = 0):
         """
         Wrapper for _assembleLiveData() to convert back the standard px_idx (eg, (0,0), (0,1), (0,2)...)
         into the index that was actually scanned at that moment.
         :param px_idx: y, x position
+        :param pxs_pos: position of center of data in m: x, y
         :param rep: x, y number of points in the scan
         For other parameters, see MultipleDetectorStream._assembleLiveData()
         """
         px_idx_flat = px_idx[0] * rep[0] + px_idx[1]
         act_px_idx = self._px_order[px_idx_flat][::-1]
         logging.debug("Converted back idx %s to %s", px_idx, act_px_idx)
-        return super()._assembleLiveData(n, raw_data, act_px_idx, rep, pol_idx)
+        return super()._assembleLiveData(n, raw_data, act_px_idx, px_pos, rep, pol_idx)
 
 
 class SpectrumArbitraryScanOrderPlugin(Plugin):
     name = "Spectrum acquisition in arbitrary scan order"
-    __version__ = "1.0"
+    __version__ = "1.1"
     __author__ = u"Éric Piel"
     __license__ = "GPLv2"
 

plugins/spectrum_raw.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-'''
+"""
 Created on 1 Sep 2023
 
 @author: Éric Piel
@@ -19,7 +19,7 @@
 
 You should have received a copy of the GNU General Public License along with Odemis. If not,
 see http://www.gnu.org/licenses/.
-'''
+"""
 
 import logging
 from collections import OrderedDict
@@ -196,9 +196,9 @@ class SEMSpectrumRawMDStream(SEMCCDMDStream):
     def _prepare(self):
         return self._sccd._prepare()
 
-    def _assembleLiveData(self, n, raw_data, px_idx, rep, pol_idx):
+    def _assembleLiveData(self, n, raw_data, px_idx, px_pos, rep, pol_idx=0):
         if n != self._ccd_idx:
-            return super()._assembleLiveData(n, raw_data, px_idx, rep, pol_idx)
+            return super()._assembleLiveData(n, raw_data, px_idx, px_pos, rep, pol_idx)
 
         # Raw data format is YC, where Y is the CCD Y... but there is already the Y of the e-beam.
         # So we report it as a T dimension, which makes the data exporter happy and Odemis viewer happy.
@@ -209,27 +209,19 @@ def _assembleLiveData(self, n, raw_data, px_idx, rep, pol_idx):
         if pol_idx > len(self._live_data[n]) - 1:
             # New polarization => new DataArray
             md = raw_data.metadata.copy()
-            # Compute metadata based on SEM metadata
-            semmd = self._live_data[0][pol_idx].metadata
-            # handle sub-pixels (aka fuzzing)
-            md[MD_PIXEL_SIZE] = (semmd[MD_PIXEL_SIZE][0] * self._emitter.resolution.value[0],
-                                 semmd[MD_PIXEL_SIZE][1] * self._emitter.resolution.value[1])
-            md[MD_POS] = semmd[MD_POS]
-
-            for k in (MD_ROTATION, MD_ROTATION_COR):
-                if k in semmd:
-                    md[k] = semmd[k]
-                else:
-                    md.pop(k, None)
-
-            md[MD_DIMS] = "CTZYX"
+            # Compute metadata to match the SEM metadata
+            center, pxs = self._get_center_pxs(rep, (1, 1), self._pxs, px_pos)
+            md.update({MD_POS: center,
+                       MD_PIXEL_SIZE: pxs,
+                       MD_DIMS: "CTZYX",
+                       MD_DESCRIPTION: self._streams[n].name.value})
+
             # Note: MD_WL_LIST is normally present.
             if MD_WL_LIST in md and spec_res != len(md[MD_WL_LIST]):
                 # Not a big deal, can happen if wavelength = 0
                 logging.warning("MD_WL_LIST is length %s, while spectrum res is %s",
                               len(md[MD_WL_LIST]), spec_res)
 
-            md[MD_DESCRIPTION] = self._streams[n].name.value
             # Make sure it doesn't contain metadata related to AR
             for k in (model.MD_AR_POLE, model.MD_AR_MIRROR_BOTTOM, model.MD_AR_MIRROR_TOP,
                       model.MD_AR_FOCUS_DISTANCE, model.MD_AR_HOLE_DIAMETER, model.MD_AR_PARABOLA_F,
@@ -260,6 +252,7 @@ def _assembleFinalData(self, n, data):
 
         self._raw.extend(data)
 
+
 # To force the "Temporal Spectrum" view to show the live stream
 TemporalSpectrumStream.register(SpectrumRawSettingsStream)
 
@@ -308,9 +301,10 @@ def _assembleFinalData(self, n, data):
     }),
 ))
 
+
 class SpectrumRawPlugin(Plugin):
     name = "Spectrum Raw acquisition"
-    __version__ = "1.0"
+    __version__ = "1.1"
     __author__ = u"Éric Piel"
     __license__ = "GPLv2"