Fixes Zeiss import

dataset.py

@@ -345,7 +345,7 @@ class DataSet(object):
             assert not self.readin
         if mode not in ['df', 'bf']:
             raise ValueError(f'mapToLength mode: {mode} not understood')
-        # pixelpos = [2110.3, 1917.5]
+
         p0 = copy(self.lastpos)
         pixelscale = self.pixelscale_df if mode == 'df' else self.pixelscale_bf
         imgdim = self.imagedim_df if mode == 'df' else self.imagedim_bf

gui/coordTransferGUI.py

 from PyQt5 import QtWidgets, QtGui, QtCore
-from typing import Tuple, TYPE_CHECKING
+from typing import Tuple, TYPE_CHECKING, List
 from copy import deepcopy
 
 from ..coordTransform import *
@@ -156,8 +156,7 @@ class CoordTransformUI(QtWidgets.QWidget):
         invertX, invertY, invertZ = self._invertGroup.getInvert()
 
         if len(srcPoints) == len(dstPoints) and len(srcPoints) >= 3 and np.all(np.isfinite(dstPoints)):
-            # if not self._dataset.coordinateSystemConfigured:
-            if True:
+            if not self._dataset.coordinateSystemConfigured:
                 self._setOriginalCoordSystem()
                 srcPoints = self._setAndGetCreatedImgMarkerSourcePoints()
 

helperfunctions.py

@@ -32,20 +32,21 @@ except ImportError:
     skimsave = None
 
 from logging import Logger
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Union
 
 if TYPE_CHECKING:
     from .instrumentcom.instrumentComBase import InstrumentComBase
 
 
-def cv2imread_fix(fname, flags=cv2.IMREAD_COLOR):
+def cv2imread_fix(fname, flags=cv2.IMREAD_COLOR) -> Union[None, np.ndarray]:
     if skimread is not None:
-        return skimread(fname, as_gray=(flags == cv2.IMREAD_GRAYSCALE))
-    with open(fname, "rb") as fp:
-        cont = fp.read()
-        img = cv2.imdecode(np.fromstring(cont, dtype=np.uint8), flags)
-        return img
-    return None
+        img = skimread(fname, as_gray=(flags == cv2.IMREAD_GRAYSCALE))
+    else:
+        img: Union[None, np.ndarray] = None
+        with open(fname, "rb") as fp:
+            cont = fp.read()
+            img = cv2.imdecode(np.fromstring(cont, dtype=np.uint8), flags)
+    return img
 
 
 def cv2imwrite_fix(fname, img, params=None):

imageimport/imageimporter.py

@@ -35,7 +35,7 @@ from ..scenePyramid import ScenePyramid
 from ..coordTransform import CoordTransfer
 
 if TYPE_CHECKING:
-    from zeissxml import Region, ZRange, Marker
+    from .zeissxml import Region, ZRange, Marker
 
 
 class ImageImporter(QtWidgets.QDialog):
@@ -55,7 +55,10 @@ class ImageImporter(QtWidgets.QDialog):
         self.zImg: Union[np.ndarray, None] = None
         self.xmlPath: str = ''
 
-        vbox = QtWidgets.QVBoxLayout()
+        self.optnLayout = QtWidgets.QVBoxLayout()
+        self.ignoreMarkersCheckbox: QtWidgets.QCheckBox = QtWidgets.QCheckBox("Ignore Markers")
+        self.ignoreMarkersCheckbox.setChecked(False)
+        self.ignoreMarkersCheckbox.toggled.connect(self._toggleMarkers)
         self.fileSelector: FileSelector = FileSelector(self)
 
         self.pointgroup = QtWidgets.QGroupBox('Marker coordinates at Raman spot [µm]', self)
@@ -119,17 +122,17 @@ class ImageImporter(QtWidgets.QDialog):
         statusLayout.addWidget(self.lblStatusZImage)
         statusLayout.addWidget(self.lblStatusMeta)
 
-        vbox.addWidget(self.fileSelector)
-        vbox.addWidget(self.pxScaleGroup)
-        vbox.addWidget(self.pointgroup)
-        vbox.addWidget(self.blurGroup)
-        vbox.addWidget(self.invertGroup)
-        vbox.addLayout(statusLayout)
-        vbox.addLayout(btnLayout)
+        self.optnLayout.addWidget(self.fileSelector)
+        self.optnLayout.addWidget(self.pxScaleGroup)
+        self.optnLayout.addWidget(self.pointgroup)
+        self.optnLayout.addWidget(self.blurGroup)
+        self.optnLayout.addWidget(self.invertGroup)
+        self.optnLayout.addLayout(statusLayout)
+        self.optnLayout.addLayout(btnLayout)
 
         self._imgPreview: ImagePreview = ImagePreview()
         hbox = QtWidgets.QHBoxLayout()
-        hbox.addLayout(vbox)
+        hbox.addLayout(self.optnLayout)
         hbox.addWidget(self._imgPreview)
         self.setLayout(hbox)
 
@@ -147,7 +150,7 @@ class ImageImporter(QtWidgets.QDialog):
         self._updateStatusLabels()
         self._enableDisableWidgets()
 
-    def setXMLPath(self, xmlPath: str) -> None:
+    def readXML(self, xmlPath: str) -> None:
         self.xmlPath = xmlPath
 
         parser = make_parser()
@@ -175,14 +178,24 @@ class ImageImporter(QtWidgets.QDialog):
             self.markers = z.markers
             self._updateStatusLabels()
             self._enableDisableWidgets()
+            self._createPointGroup()
 
     def _createPointGroup(self) -> None:
+        self._clearLayout(self.pointgroup.layout())
+        pointGroupInd: int = self.optnLayout.indexOf(self.pointgroup)
+        self.optnLayout.removeWidget(self.pointgroup)
+        self.pointgroup.setParent(None)
+
+        self.pointgroup = QtWidgets.QGroupBox('Marker coordinates at Raman spot [µm]', self)
         self.points = PointCoordinates(len(self.markers), self.instrctrl, self,
                                        names=[m.name for m in self.markers])
         self.points.pimageOnly.setVisible(False)
-        self.pointgroup.setLayout(self.points)
         self.points.readPoint.connect(self.takePoint)
 
+        self.pointgroup.setLayout(self.points)
+        self.optnLayout.insertWidget(pointGroupInd, self.ignoreMarkersCheckbox)
+        self.optnLayout.insertWidget(pointGroupInd+1, self.pointgroup)
+
     @QtCore.pyqtSlot(float, float, float)
     def takePoint(self, x, y, z):
         points = self.points.getPoints()
@@ -193,14 +206,12 @@ class ImageImporter(QtWidgets.QDialog):
         fname = QtWidgets.QFileDialog.getSaveFileName(self, 'Create New GEPARD Project', defaultPath, '*.pkl')[0]
         colorImg: np.ndarray = self._imgPreview.getImage()
         if fname != '':
-            abort: bool = True
             dataset = DataSet(fname, newProject=True)
             requiresCoordTransfer = False
-            if None not in [self.zImg, self.markers, self.zrange]:
-                T, pc, zpc, accept = self.getTransform()
-                if accept:
-                    self.convertZimg(dataset, T, pc, zpc)
-                    abort = False
+            if self.zImg is not None and self.markers is not None and self.zrange is not None:
+                abort = self.convertZimg(dataset)
+                if self.ignoreMarkersCheckbox.isChecked():
+                    requiresCoordTransfer = True
             else:
                 self._set_ZValImageToDataset(dataset, np.zeros(colorImg.shape[:2]))
                 dataset.importedWithPlaceholderZValImg = True
@@ -220,7 +231,27 @@ class ImageImporter(QtWidgets.QDialog):
             else:
                 QtWidgets.QMessageBox.critical(self, "Error", "Failed importing project...")
 
-    def convertZimg(self, dataset, T, pc, zpc):
+    def convertZimg(self, dataset) -> bool:
+        """
+        Converts the zvalImage and sets coordinate system, if marker shall be used.
+        Returns whether or not to abort the import process. Can be True, if transform residues are too large..
+        """
+        if self.ignoreMarkersCheckbox.isChecked():
+            T, pc, zpc, accept = None, None, np.array([0, 0, 0]), True
+        else:
+            T, pc, zpc, accept = self.getTransform()
+
+            newTransform: CoordTransfer = CoordTransfer()
+            newTransform.rotMatrix = T
+            newTransform.offset = pc
+            dataset.coordinatetransform = newTransform
+
+            # set image center as reference point (assume just one tile)
+            # in data set (use Zeiss coordinates)
+            p0center = np.array([self.region.centerx, self.region.centery]) - zpc[:2]
+            dataset.lastpos = p0center
+            dataset.readin = False
+
         N = int(round(abs(self.zrange.zn - self.zrange.z0) / self.zrange.dz))
         z0, zn = self.zrange.z0, self.zrange.zn
         if zn < z0:
@@ -232,9 +263,11 @@ class ImageImporter(QtWidgets.QDialog):
         dataset.heightmapParams = np.zeros(3)
         dataset.signy = 1.
         zimg = self.zImg
-        print("zimg shape:", zimg.shape, flush=True)
         radius = self.blurspinbox.value()
         blur = cv2.GaussianBlur(zimg, (radius, radius), 0)
+        blur = np.clip(blur * 255.0, 0, 255.0)
+        blur[np.isnan(blur)] = 0.
+        blur = np.uint8(blur)
 
         pshift = self.instrctrl.getSpectrumPositionShift()
         dataset.pshift = pshift
@@ -242,29 +275,14 @@ class ImageImporter(QtWidgets.QDialog):
 
         # use input image as single image aquired in one shot
         dataset.pixelscale_df = dataset.pixelscale_bf = pixelscale
+        dataset.zvalimg = blur
         dataset.calculateImageDimsFromZImg()
-        print('scale:', pixelscale)
-        print('dim df:', dataset.imagedim_df)
-        print('dim bf:', dataset.imagedim_bf)
-
-        newTransform: CoordTransfer = CoordTransfer()
-        newTransform.rotMatrix = T
-        newTransform.offset = pc
-        dataset.coordinatetransform = newTransform
-
-        # set image center as reference point (assume just one tile) 
-        # in data set (use Zeiss coordinates)
-        p0center = np.array([self.region.centerx, self.region.centery]) - zpc[:2]
-        dataset.readin = False
-        dataset.lastpos = p0center
-        # Originally, here was also a line to set dataset.maxdim = p0center. maxdim is not needed here, though (optical
-        # scan is not done anymore... Also, maxdim should contain x and y coordinates of TWO points...???
 
-        blur = np.clip(blur * 255.0, 0, 255.0)
-        blur[np.isnan(blur)] = 0.
-        blur = np.uint8(blur)
         self._set_ZValImageToDataset(dataset, blur)
 
+        abort: bool = not accept
+        return abort
+
     def _set_ZValImageToDataset(self, dataset: 'DataSet', zvalImg: np.ndarray) -> None:
         zimgname = dataset.getZvalImageName()
         cv2imwrite_fix(zimgname, zvalImg)
@@ -330,17 +348,28 @@ class ImageImporter(QtWidgets.QDialog):
         return T, pc - shift, zpc, accept
 
     def enableDisablePxScaleGroup(self, enabled: bool) -> None:
+        self._clearLayout(self.pxScaleGroup.layout())
+        pxScaleGroupInd: int = self.optnLayout.indexOf(self.pxScaleGroup)
+        self.optnLayout.removeWidget(self.pxScaleGroup)
+        self.pxScaleGroup.setParent(None)
+
         layout: QtWidgets.QHBoxLayout = QtWidgets.QHBoxLayout()
         if enabled:
             layout.addWidget(self.pxScaleSpinbox)
         else:
             layout.addWidget(QtWidgets.QLabel("Will be read from MetaFile"))
         layout.addStretch()
+        self.pxScaleGroup: QtWidgets.QGroupBox = QtWidgets.QGroupBox("Pixelscale (µm/px)")
         self.pxScaleGroup.setLayout(layout)
         self.pxScaleGroup.setEnabled(enabled)
 
+        self.optnLayout.insertWidget(pxScaleGroupInd, self.pxScaleGroup)
+
     def _enableDisableWidgets(self) -> None:
-        self.pconvert.setEnabled(self.colorImg is not None)
+        enabled: bool = self.colorImg is not None
+        self.pconvert.setEnabled(enabled)
+        self.invertGroup.setEnabled(enabled)
+        self.blurGroup.setEnabled(enabled)
 
     def _updateStatusLabels(self) -> None:
         if self.colorImg is None:
@@ -364,6 +393,24 @@ class ImageImporter(QtWidgets.QDialog):
             self.lblStatusMeta.setStyleSheet("color: green")
             self.lblStatusMeta.setText("Metadata loaded.")
 
+    def _toggleMarkers(self) -> None:
+        """
+        Sets Marker group enabled or disabled, according to the checkbox.
+        """
+        self.pointgroup.setDisabled(self.ignoreMarkersCheckbox.isChecked())
+
+    def _clearLayout(self, layout) -> None:
+        """
+        Deletes all contents of the given layout.
+        """
+        for i in reversed(range(layout.count())):
+            item = layout.itemAt(i)
+            if item is not None:
+                widget = item.widget()
+                layout.removeWidget(widget)
+            else:
+                layout.removeItem(item)
+
 
 class FileSelector(QtWidgets.QGroupBox):
     def __init__(self, parent: 'ImageImporter'):
@@ -419,6 +466,7 @@ class FileSelector(QtWidgets.QGroupBox):
         if fname:
             try:
                 image: np.ndarray = cv2imread_fix(fname)
+                print('loaded colorImg with shape:', image.shape)
                 self._LineEditImage.setText(os.path.basename(fname))
                 self._parent.setColorImage(image)
             except Exception as e:
@@ -429,9 +477,12 @@ class FileSelector(QtWidgets.QGroupBox):
                                                          filter="Images (*.tiff *tif)")
         if fname:
             try:
-                zImage: np.ndarray = cv2imread_fix(fname)
+                zImage: np.ndarray = cv2imread_fix(fname, cv2.IMREAD_GRAYSCALE)
+                print('loaded zImg with shape:', zImage.shape)
                 self._LineEditZImage.setText(os.path.basename(fname))
+                print('set Text')
                 self._parent.setZValImage(zImage)
+                print('set zvalImage to Parent')
             except Exception as e:
                 QtWidgets.QMessageBox.warning(self, "Error", f"ZImage {fname} could not be loaded:/n{e}")
 
@@ -440,10 +491,12 @@ class FileSelector(QtWidgets.QGroupBox):
                                                          filter="XML File (*.xml)")
         if fname:
             self._LineEditMeta.setText(os.path.basename(fname))
-            self._parent.setXMLPath(fname)
-            self._parent.enableDisablePxScaleGroup(True)
-        else:
+            self._parent.readXML(fname)
+            print('finished reading XML')
             self._parent.enableDisablePxScaleGroup(False)
+        else:
+            self._parent.enableDisablePxScaleGroup(True)
+
 
 
 class ImagePreview(QtWidgets.QWidget):

instrumentcom/FTIRCom.py

@@ -149,7 +149,10 @@ class FTIRCom(InstrumentComBase):
         self.dde.set_stage_z(z)
         x_set, y_set, z_set = self.dde.get_stage_coords()
         diffz: float = abs(z_set - z)
-        assert diffz <= epsz, f'diff z is {diffz}, max allowed: {epsz}'
+        if diffz > epsz:
+            self.logger.critical(f"Warning, z difference is large! z-target: {z}, z_actul: {z_set}, diff: {diffz} (max. allowed: {epsz}).")
+            breakpoint()
+        # assert diffz <= epsz, f'diff z is {diffz}, max allowed: {epsz}'
 
     def setAperture(self, widthMicrons: float, heightMicrons: float, angleDegree: float) -> None:
         self.dde.set_aperture(widthMicrons, heightMicrons, angleDegree)

requirements.txt

@@ -16,7 +16,8 @@ pyparsing==2.4.7
 python-dateutil==2.8.1
 pytz==2020.1
 pywavelets==1.1.1
-pywin32~=2.2.7
+PyQt5
+jcamp
 scikit-fuzzy==0.4.2
 scikit-image==0.17.2
 scipy==1.5.2