Commit cfa964ed authored by JosefBrandt's avatar JosefBrandt
Browse files

temporary fixes, non working solution

parent f1fe95fd

ramancom/simulatedraman.py

+6 −3
Original line number Diff line number Diff line
@@ -21,6 +21,8 @@ If not, see <https://www.gnu.org/licenses/>. 
Simualted Raman interface module for testing without actual raman system connected

"""



import sys

stdout = sys.stdout

from time import sleep

import numpy as np

from shutil import copyfile
@@ -35,9 +37,9 @@ class SimulatedRaman(RamanBase): 
        self.currentpos = None, 0., 0.

        self.currentZ = 0.

        # some plausible data to simulate consecutively changing positions

        self.positionlist = np.array([[ 1526. , -1379.9,  -131. ],

                                      [ 3762.5, -1197.7,  -138.1],

                                      [ 2313.7, -2627.2,  -138.1],

        self.positionlist = np.array([[ -12012,  13716,  -1290],

                                      [ -11955,  -9200,  -1279],

                                      [  10978,  -9254,  -1297],

                                      [ 2704.1, -1788.2,  -138.1],

                                      [ 3884. , -2650.8,  -138.1]])

        self.znum = 4
@@ -77,6 +79,7 @@ class SimulatedRaman(RamanBase): 
        

    def moveToAbsolutePosition(self, x, y, z=None, epsxy=0.11, epsz=0.011, debugReturn=False, measurementRunning=False):

        assert self.connected

        print('moving to:', x, y, z, file=stdout)

        if z is None:

            self.currentpos = x, y, self.currentpos[2]        

        else:

viewitems.py

+44 −42
Original line number Diff line number Diff line
@@ -113,6 +113,7 @@ class SegmentationContours(QtWidgets.QGraphicsItem): 
            self.update()

    

    def contextMenuEvent(self, event):

        if self.parent.analysiswidget is not None:

            contextMenu = QtWidgets.QMenu("Particle options")

    

            combineMenu = QtWidgets.QMenu("Combine Particles into")
@@ -129,6 +130,7 @@ class SegmentationContours(QtWidgets.QGraphicsItem): 
            

            reassignActs = []

            reassignMenu = QtWidgets.QMenu("Reassign particle(s) into")

            

            for polymer in self.parent.analysiswidget.datastats.getUniquePolymers():

                reassignActs.append(reassignMenu.addAction(polymer))

            reassignActs.append(reassignMenu.addAction("other"))

zeissimporter.py

+4 −2
Original line number Diff line number Diff line
@@ -186,10 +186,12 @@ class ZeissImporter(QtWidgets.QDialog): 
        dataset.coordinatetransform = T, pc

        

        # set image center as reference point in data set (use Zeiss coordinates)

        p0 = np.array([self.region.centerx, self.region.centery]) - zpc[:2]

        p0center = np.array([self.region.centerx, self.region.centery]) - zpc[:2]

        p0 = p0center-.5*np.array((self.region.width, self.region.height))

        p1 = p0center+.5*np.array((self.region.width, self.region.height))

        dataset.readin = False

        dataset.lastpos = p0

        dataset.maxdim = p0 + p0

        dataset.maxdim = p0 + p1

        

        zmin, zmax = dataset.zpositions.min(), dataset.zpositions.max()

        blur = (blur)*(255.)