Downscale video image

A scaling factor can be indicated in the gepard.cfg

.gitignore

@@ -28,3 +28,5 @@ instrumentcom/renishawtesting.py
 *.pyc
 
 *.jdx
+
+instrumentcom/thermoFTIRCom.py

gepard_ConfigTemplate.cfg

@@ -11,6 +11,8 @@ raman_interface = SIMULATED_RAMAN_CONTROL
 
 [General Microscope Setup]
 magnification = 20
+# The scale factor allows downscaling the video image of the microscope camera in order to reduce final image size
+videoImageScaleFactor = 1.0
 
 [Renishaw]
 #information specific for renishaw control

gui/opticalscanui.py

@@ -29,19 +29,20 @@ import logging.handlers
 import cv2
 from time import localtime, strftime
 from typing import List, TYPE_CHECKING
-from ..imagestitch import imageStacking
-from ..helperfunctions import cv2imread_fix, cv2imwrite_fix, getInstrumentControl, positionWidgetOnScreen
-from ..opticalbackground import BackGroundManager
 from .uielements import TimeEstimateProgressbar
 from .zlevelsetter import ZLevelSetter
+from ..imagestitch import imageStacking
+from ..helperfunctions import cv2imread_fix, cv2imwrite_fix, positionWidgetOnScreen
+from ..opticalbackground import BackGroundManager
 from ..scenePyramid import ScenePyramid
 from ..gepardlogging import setDefaultLoggingConfig
+from ..instrumentcom.instrumentComBase import InstrumentComBase
 
 if TYPE_CHECKING:
     from ..sampleview import SampleView
 
 
-def scan(path, sol, zpositions, grid, controlclass, dataqueue,
+def scan(path, sol, zpositions, grid, instrctrlClass, videoScaleFac: float, dataqueue,
          stopevent, logpath, ishdr=False):
     if ishdr:
         merge_mertens = cv2.createMergeMertens()
@@ -55,7 +56,8 @@ def scan(path, sol, zpositions, grid, controlclass, dataqueue,
     logger.info('starting new optical scan')
       
     try:
-        instrctrl = controlclass(logger)
+        instrctrl: InstrumentComBase = instrctrlClass(logger)
+        instrctrl.setVideoScaleFactor(videoScaleFac)
         instrctrl.updateImageConfig(os.path.dirname(logpath))
         instrctrl.connect()
         zlist = list(enumerate(zpositions))
@@ -707,7 +709,7 @@ class OpticalScanUI(QtWidgets.QWidget):
             self.dataqueue = Queue()
             logpath = os.path.join(self.dataset.path, 'opticalScanLog.txt')
             self.process = Process(target=scan, args=(path, sol, self.dataset.zpositions, 
-                                self.dataset.grid, self.instrctrl.__class__,
+                                self.dataset.grid, self.instrctrl.__class__, self.instrctrl.videoScaleFactor,
                                 self.dataqueue, self.processstopevent, 
                                 logpath, self.hdrcheck.isChecked()))
             self.process.start()

helperfunctions.py

@@ -22,7 +22,6 @@ If not, see <https://www.gnu.org/licenses/>.
 import numpy as np
 import cv2
 import os
-import sys
 from PyQt5 import QtWidgets, QtCore
 
 try:
@@ -32,8 +31,10 @@ except ImportError:
     skimread = None
     skimsave = None
 
-from .instrumentcom.instrumentComBase import InstrumentComBase
 from logging import Logger
+from typing import TYPE_CHECKING
+if TYPE_CHECKING:
+    from .instrumentcom.instrumentComBase import InstrumentComBase
 
 
 def cv2imread_fix(fname, flags=cv2.IMREAD_COLOR):
@@ -105,11 +106,12 @@ def polygoncovering(boundary, wx, wy):
     return poslist
 
 
-def getInstrumentControl(controlclass: InstrumentComBase, logger: Logger) -> InstrumentComBase:
+def getInstrumentControl(controlclass: 'InstrumentComBase', logger: Logger) -> 'InstrumentComBase':
     simulatedInterface: bool = False
     if 'simulatedInterface' in controlclass.__dict__.keys():
         if controlclass.__dict__['simulatedInterface'] == True:
             simulatedInterface = True
+
     if simulatedInterface:
         instrctrl = controlclass(logger, ui=False)
     else:
@@ -131,7 +133,7 @@ def needsFTIRAperture(sampleview) -> bool:
     return needsAperture
 
 
-def lightModeSwitchNeeded(instrctrl: InstrumentComBase) -> bool:
+def lightModeSwitchNeeded(instrctrl: 'InstrumentComBase') -> bool:
     switchNeeded: bool = False
     if instrctrl.name == 'RenishawCOM':
         instrctrl.connect()

instrumentcom/WITecCOM.py

@@ -380,6 +380,7 @@ class WITecCOM(InstrumentComBase):
         self.ImageNameMan.SetValue(fname)
         self.ImageSaveMan.OperateTrigger()
         sleep(.1)
+        self._scaleVideoImage(fname)
 
     @comErrorRepeater
     def getImageDimensions(self, mode = 'df'):

instrumentcom/instrumentComBase.py

@@ -18,15 +18,32 @@ You should have received a copy of the GNU General Public License
 along with this program, see COPYING.  
 If not, see <https://www.gnu.org/licenses/>.
 """
+import cv2
+from ..helperfunctions import cv2imread_fix, cv2imwrite_fix
 
 
 class InstrumentComBase(object):
+    videoScaleFactor: float = 1.0
+
+    @classmethod
+    def setVideoScaleFactor(cls, newFac) -> None:
+        cls.videoScaleFactor = float(newFac)
+
     def __init__(self, logger=None):
         self.name = None
         self.connected = False
         self.timeseries = False
         self.logger = logger
 
+    def _scaleVideoImage(self, imagePath: str) -> None:
+        """
+        For convenience.. Takes the image at the indicated path and scales it to the videoScaleFactor.
+        """
+        img = cv2imread_fix(imagePath)
+        img = cv2.resize(img, None, fx=self.videoScaleFactor, fy=self.videoScaleFactor)
+        img = cv2.cvtColor(img, cv2.COLOR_RGB2BGR)
+        cv2imwrite_fix(imagePath, img)
+
     def getRamanPositionShift(self):
         """ Compute the shift between laser spot and image center"""
         raise NotImplementedError
@@ -61,10 +78,6 @@ class InstrumentComBase(object):
         """
         raise NotImplementedError
         
-    # IT IS NOT NEEDED, ISN'T IT??
-    # def startSinglePointScan(self):
-    #     raise NotImplementedError
-        
     def initiateMeasurement(self, specScanSettings):
         raise NotImplementedError
         

instrumentcom/instrumentConfig.py

@@ -29,6 +29,7 @@ config = configparser.ConfigParser()
 config.read(os.path.join(defaultPath, 'gepard.cfg'))
 
 interface = "SIMULATED_RAMAN_CONTROL"
+videoImgScale = 1.0
 
 
 class SpecScanParameter(object):
@@ -63,7 +64,6 @@ class SpecScanParameter(object):
 
 try: 
     defaultPath = config["Defaults"]["file_path"]
-    print('default Path is now:', defaultPath)
 except KeyError:
     pass
 
@@ -72,6 +72,12 @@ try:
 except KeyError:
     pass
 
+try:
+    videoImgScale = config["General Microscope Setup"]["videoImageScaleFactor"]
+except KeyError:
+    pass
+
+
 if interface == "SIMULATED_RAMAN_CONTROL":
     from .simulated.simulatedraman import SimulatedRaman
     InstrumentControl = SimulatedRaman
@@ -95,7 +101,6 @@ elif interface == "RENISHAW_CONTROL":
         InstrumentControl.cam_df_dims = [float(df_dims[0]), float(df_dims[1])]
     except:
         print('Invalid image dimensions in config file!')
-#    InstrumentControl.defaultMeasTemplate = config["Renishaw"]["defaultMeasTemplate"]
     InstrumentControl.measTemplatePath = config["Renishaw"]["measTemplatePath"]
     print(InstrumentControl.measTemplatePath)
     InstrumentControl.specScanParameters = InstrumentControl.updateSpecScanParameters(InstrumentControl, InstrumentControl.measTemplatePath)
@@ -106,3 +111,5 @@ elif interface == "THERMO_FTIR":
     from .thermoFTIRCom import ThermoFTIRCom
     InstrumentControl = ThermoFTIRCom
     simulatedRaman = False
+
+InstrumentControl.setVideoScaleFactor(videoImgScale)

instrumentcom/simulated/imageGenerator.py

@@ -122,12 +122,8 @@ class FakeParticle:
 class FakeCamera:
     # TODO: Implement a small angle to simulate a tilted camera!
     def __init__(self):
-        self.imgDims: Tuple[int, int] = (500, 250)  # width, height of camera imgage
+        self.imgDims: Tuple[int, int] = (600, 350)  # width, height of camera imgage in pixel
         self.pixelscale: float = 1.0  # µm/px
-        self.sizeScale: float = 100.0  # smaller values make particles rendered smaller and vice versa
-        self.threshold: float = 0.7  # threshold for determining particles. Larger values -> smaller particles
-        self.numZLevels: int = 7  # number of z-levels cached for faking depth of field
-        self.maxZDiff: float = 100  # max difference in z that is simulated.
         self.currentImage: np.ndarray = np.zeros((self.imgDims[1], self.imgDims[0], 3))
         self.fakeFilter: FakeFilter = FakeFilter()
 

instrumentcom/simulated/simulatedStage.py

@@ -26,7 +26,7 @@ import cv2
 import json
 import numpy as np
 from typing import List
-from .imageGenerator import FakeCamera
+from .imageGenerator import FakeCamera, FakeFilter
 from ..instrumentComBase import InstrumentComBase
 from ...helperfunctions import getAppFolder
 
@@ -266,23 +266,23 @@ class SimulatedStageUI(QtWidgets.QWidget):
         
         self.stageParent.moveToPosition(newPos[0], newPos[1], newPos[2])
 
-    def _moveToPresetPosition(self, btn: QtWidgets.QPushButton, stepSize: float = 1000) -> None:
+    def _moveToPresetPosition(self, btn: QtWidgets.QPushButton) -> None:
         label: str = btn.text()
+        filter: FakeFilter = self.stageParent.camera.fakeFilter
+        margin: float = 0.9
         newPos: List[float] = [0.0, 0.0, 0.0]
         if label == 'UpperLeft':
-            newPos[0] -= stepSize
-            newPos[1] += stepSize
+            newPos[0] = filter.xRange[0] * margin
+            newPos[1] = filter.yRange[1] * margin
         elif label == 'UpperRight':
-            newPos[0] += stepSize
-            newPos[1] += stepSize
+            newPos[0] = filter.xRange[1] * margin
+            newPos[1] = filter.yRange[1] * margin
         elif label == 'LowerLeft':
-            newPos[0] -= stepSize
-            newPos[1] -= stepSize
+            newPos[0] = filter.xRange[0] * margin
+            newPos[1] = filter.yRange[0] * margin
         elif label == 'LowerRight':
-            newPos[0] += stepSize
-            newPos[1] -= stepSize
-        elif label == 'Center':
-            pass
+            newPos[0] = filter.xRange[1] * margin
+            newPos[1] = filter.yRange[0] * margin
 
         self.stageParent.moveToPosition(newPos[0], newPos[1], newPos[2])
 

instrumentcom/simulated/simulatedraman.py

@@ -43,7 +43,6 @@ class SimulatedRaman(InstrumentComBase):
         self.znum = 4
         self.gridnum = 36
         self.positionindex = 0
-        self.imageindex = 0
         
     def getRamanPositionShift(self):
         return 0., 0.
@@ -51,7 +50,6 @@ class SimulatedRaman(InstrumentComBase):
     def connect(self):
         self.stage.connect()
         self.connected = True
-        self.imageindex = 0
         return True
     
     def disconnect(self):
@@ -84,7 +82,7 @@ class SimulatedRaman(InstrumentComBase):
     def saveImage(self, fname):
         assert self.connected
         cv2imwrite_fix(fname, self.stage.getCurrentCameraImage())
-        self.imageindex = (self.imageindex+1) % (self.znum*self.gridnum)
+        self._scaleVideoImage(fname)
         
     def getImageDimensions(self, mode='df'):
         """ 
@@ -92,7 +90,9 @@ class SimulatedRaman(InstrumentComBase):
         """
         assert self.connected
         camDims: tuple = self.stage.camera.imgDims
-        return camDims[0], camDims[1], 0  # TODO: RE-Implement a small angle to simulate a tilted camera!
+        # TODO: RE-Implement a small angle to simulate a tilted camera!
+        angle: float = 0.0
+        return camDims[0], camDims[1], angle
     
     def startSinglePointScan(self):
         assert self.connected

unittests/test_gepard.py

@@ -12,20 +12,18 @@ from typing import TYPE_CHECKING
 from ..sampleview import SampleView
 from ..dataset import DataSet
 from ..analysis.particleContainer import ParticleContainer
-from ..analysis.particleAndMeasurement import Measurement
 from ..instrumentcom.instrumentComBase import InstrumentComBase
-from ..instrumentcom.instrumentConfig import defaultPath
+from ..instrumentcom.simulated.simulatedStage import SimulatedStage
 from ..gui.opticalscanui import OpticalScanUI, PointCoordinates
 from ..gui.detectionview import ParticleDetectionView, ImageView
 from ..gui.specscanui import SpecScanUI
-from ..gui.viewItems.detectItems import SeedPoint
 from ..gui.viewItemHandler import ViewItemHandler
 from ..workmodes import ModeHandler, ModeOpticalScan, ModeParticleDetection, ModeSpectrumScan
+
 if TYPE_CHECKING:
     from ..__main__ import GEPARDMainWindow
 
 
-
 def testGepard(gepard):
     gepard.testCase = TestGepard(gepard)
     gepard.testCase.start_automated_test()
@@ -67,17 +65,19 @@ class TestGepard(unittest.TestCase):
 
         # SET UP OPTICAL SCAN
         moveMargin: int = 300
-        curPos: tuple = self.instrctrl.getPosition()
         self.assertEqual(type(self.modeHandler.activeMode), ModeOpticalScan)
         oscanWidget: OpticalScanUI = self.modeHandler.oscanMode.widget
         self.assertEqual(type(oscanWidget), OpticalScanUI)
         self.assertTrue(oscanWidget.isVisible())
         oscanWidget.zLevelSetter.numLevelsSpinbox.setValue(3)
+        simulatedStage: SimulatedStage = self.sampleview.instrctrl.stage
+        simulatedStage.moveToPosition(0, 0, 0)
+
         points: PointCoordinates = oscanWidget.points
         points.read(0)
-        self.instrctrl.moveToAbsolutePosition(curPos[0] + moveMargin, curPos[1] + moveMargin, curPos[2])
+        self.instrctrl.moveToAbsolutePosition(moveMargin, moveMargin, 0)
         points.read(1)
-        self.instrctrl.moveToAbsolutePosition(curPos[0] - moveMargin, curPos[1] - moveMargin, curPos[2])
+        self.instrctrl.moveToAbsolutePosition(-moveMargin, -moveMargin, 0)
         points.read(2)
 
         oscanWidget.pareaselect.click()