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Commit 34439505 authored by Josef Brandt's avatar Josef Brandt
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Merge branch 'CoordinateTransfer' into MergingIntoTiling2Develop

parents 11fdf4ed 228a27cc
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Showing with 570 additions and 119 deletions
__main__.py
View file @ 34439505
......@@ -83,8 +83,7 @@ class GEPARDMainWindow(QtWidgets.QMainWindow):
@QtCore.pyqtSlot()
def open(self, fileName=False):
if fileName is False:
fileName = QtWidgets.QFileDialog.getOpenFileName(self, "Open Project",
defaultPath, "*.pkl")[0]
fileName = QtWidgets.QFileDialog.getOpenFileName(self, "Open Project", defaultPath, "*.pkl")[0]
if fileName:
self.fname = str(fileName)
self.view.open(self.fname)
......@@ -204,6 +203,10 @@ class GEPARDMainWindow(QtWidgets.QMainWindow):
self.configRamanCtrlAct.triggered.connect(self.view.configureRamanControl)
if self.view.simulatedRaman:
self.configRamanCtrlAct.setDisabled(True)
self.recalculateCoordAct = QtWidgets.QAction("&Recalculate Coordinate System")
self.recalculateCoordAct.setDisabled(True)
self.recalculateCoordAct.triggered.connect(self.view.recalculateCoordinateSystem)
self.noOverlayAct = QtWidgets.QAction("&No Overlay", self)
self.noOverlayAct.setShortcut("1")
......@@ -224,18 +227,18 @@ class GEPARDMainWindow(QtWidgets.QMainWindow):
def updateModes(self, active=None, maxenabled=None):
ose, osc, pde, pdc, rse, rsc = [False]*6
if maxenabled=="OpticalScan":
if maxenabled == "OpticalScan":
ose = True
elif maxenabled=="ParticleDetection":
elif maxenabled == "ParticleDetection":
ose, pde = True, True
elif maxenabled=="RamanScan":
elif maxenabled == "RamanScan":
ose, pde, rse = True, True, True
if active=="OpticalScan" and ose:
if active == "OpticalScan" and ose:
osc = True
elif active=="ParticleDetection" and pde:
elif active == "ParticleDetection" and pde:
pdc = True
elif active=="RamanScan" and rse:
elif active == "RamanScan" and rse:
rsc = True
self.opticalScanAct.setEnabled(ose)
......@@ -293,6 +296,7 @@ class GEPARDMainWindow(QtWidgets.QMainWindow):
self.toolsMenu = QtWidgets.QMenu("&Tools")
self.toolsMenu.addAction(self.snapshotAct)
self.toolsMenu.addAction(self.configRamanCtrlAct)
self.toolsMenu.addAction(self.recalculateCoordAct)
self.dispMenu = QtWidgets.QMenu("&Display", self)
self.overlayActGroup = QtWidgets.QActionGroup(self.dispMenu)
......@@ -334,6 +338,7 @@ class GEPARDMainWindow(QtWidgets.QMainWindow):
self.toolbar.setOrientation(QtCore.Qt.Vertical)
self.addToolBar(QtCore.Qt.LeftToolBarArea, self.toolbar)
if __name__ == '__main__':
import sys
from time import localtime, strftime
......
dataset.py
View file @ 34439505
......@@ -24,6 +24,7 @@ import numpy as np
import sys
import cv2
from copy import copy
from typing import List
from .analysis.particleContainer import ParticleContainer
from .legacyConvert import legacyConversion, currentVersion
from .helperfunctions import cv2imwrite_fix, cv2imread_fix
......@@ -31,9 +32,11 @@ from .helperfunctions import cv2imwrite_fix, cv2imread_fix
# (no relative import)
from . import dataset
from . import analysis
from .coordinatetransform import TrayMarker, ImageMarker
sys.modules['dataset'] = dataset
sys.modules['analysis'] = analysis
def loadData(fname):
retds = None
with open(fname, "rb") as fp:
......@@ -120,11 +123,11 @@ class DataSet(object):
self.version = currentVersion
self.lastpos = None
self.maxdim = None
self.pixelscale_df = None # µm / pixel --> scale of DARK FIELD camera (used for image stitching)
self.pixelscale_bf = None # µm / pixel of DARK FIELD camera (set to same as bright field, if both use the same camera)
self.pixelscale_df = None # µm / pixel --> scale of DARK FIELD camera (used for image stitching)
self.pixelscale_bf = None # µm / pixel of DARK FIELD camera (set to same as bright field, if both use the same camera)
self.imagedim_bf = None # width, height, angle of BRIGHT FIELD camera
self.imagedim_df = None # width, height, angle of DARK FIELD camera (set to same as bright field, if both use the same camera)
self.imagescanMode = 'df' #was the fullimage acquired in dark- or brightfield?
self.imagescanMode = 'df' # was the fullimage acquired in dark- or brightfield?
self.fitpoints = [] # manually adjusted positions aquired to define the specimen geometry
self.fitindices = [] # which of the five positions in the ui are already known
self.boundary = [] # scan boundary computed by a circle around the fitpoints + manual adjustments
......@@ -132,7 +135,9 @@ class DataSet(object):
self.zpositions = [] # z-positions for optical scan
self.heightmap = None
self.zvalimg = None
self.coordinatetransform = None # if imported form extern source coordinate system may be rotated
self.coordinatetransform = None # if imported form extern source coordinate system may be rotated
self.trayMarkers: List[TrayMarker] = [] # list of markers on the sample tray
self.imageMarkers: List[ImageMarker] = [] # list of coordinate markers within the image
self.signx = 1.
self.signy = -1.
......@@ -141,7 +146,6 @@ class DataSet(object):
# parameters specifically for raman scan
self.pshift = None # shift of raman scan position relative to image center
self.coordOffset = [0, 0] #offset of entire coordinate system
self.seedpoints = np.array([])
self.seeddeletepoints = np.array([])
self.detectParams = {'points': np.array([[50,0],[100,200],[200,255]]),
......@@ -219,31 +223,31 @@ class DataSet(object):
p0 = copy(self.lastpos)
if self.coordinatetransform is not None:
z = 0. if len(p)<3 else p[2]
z = 0. if len(p) < 3 else p[2]
T, pc = self.coordinatetransform
p = (np.dot(np.array([p[0], p[1], z])-pc, T.T))
if mode == 'df':
p0[0] -= self.signx*self.imagedim_df[0]/2
p0[1] -= self.signy*self.imagedim_df[1]/2
x, y = self.signx*(p[0] - p0[0])/self.pixelscale_df, self.signy*(p[1] - p0[1])/self.pixelscale_df
elif mode == 'bf':
p0[0] -= self.signx*self.imagedim_bf[0]/2
p0[1] -= self.signy*self.imagedim_bf[1]/2
x, y = self.signx*(p[0] - p0[0])/self.pixelscale_bf, self.signy*(p[1] - p0[1])/self.pixelscale_bf
else:
raise ValueError(f'mapToPixel mode: {mode} not understood')
assert mode in ['df', 'bf'], f'mapToPixel mode: {mode} not understood'
pixelscale: float = self.pixelscale_bf if mode == 'bf' else self.pixelscale_df
p0[0] -= self.signx*self.imagedim_df[0]/2
p0[1] -= self.signy*self.imagedim_df[1]/2
x, y = self.signx*(p[0] - p0[0])/pixelscale, self.signy*(p[1] - p0[1])/pixelscale
# TODO: SANITY CHECK AT REAL INSTRUMENT IF THE BELOW CODE CAN BE REMOVED (WAS SUBSTITUTED BY THE 4 LINES ABOVE)
# if mode == 'df':
# p0[0] -= self.signx*self.imagedim_df[0]/2
# p0[1] -= self.signy*self.imagedim_df[1]/2
# x, y = self.signx*(p[0] - p0[0])/self.pixelscale_df, self.signy*(p[1] - p0[1])/self.pixelscale_df
#
# elif mode == 'bf':
# p0[0] -= self.signx*self.imagedim_bf[0]/2
# p0[1] -= self.signy*self.imagedim_bf[1]/2
# x, y = self.signx*(p[0] - p0[0])/self.pixelscale_bf, self.signy*(p[1] - p0[1])/self.pixelscale_bf
return x, y
def mapToLength(self, pixelpos, mode='df', force=False, returnz=False):
if not force:
assert not self.readin
p0 = copy(self.lastpos)
p0[0] += self.coordOffset[0]
p0[1] += self.coordOffset[1]
if mode == 'df':
p0[0] -= self.signx*self.imagedim_df[0]/2
p0[1] -= self.signy*self.imagedim_df[1]/2
......@@ -262,7 +266,7 @@ class DataSet(object):
if self.coordinatetransform is not None:
T, pc = self.coordinatetransform
x, y, z = (np.dot(np.array([x,y,z]), T) + pc)
x, y, z = (np.dot(np.array([x, y, z]), T) + pc)
if returnz:
return x, y, z
......
gui/coordTransferGUI.py 0 → 100644
View file @ 34439505
from PyQt5 import QtWidgets, QtGui, QtCore
import numpy as np
from typing import List
from copy import deepcopy
from ..coordinatetransform import ImageMarker, TrayMarker, getTransform
from ..ramancom.ramanbase import RamanBase
class CoordTransformUI(QtWidgets.QWidget):
def __init__(self, viewParent):
super(CoordTransformUI, self).__init__()
self.setWindowTitle('Recalculate Coordinate System')
self.setWindowFlags(QtCore.Qt.WindowStaysOnTopHint)
self.viewParent = viewParent
self.ramanctrl: RamanBase = self.viewParent.ramanctrl
self.imageMarkers: List[ImageMarker] = [] # in the new coord system
self.newImageMarkers: List[ImageMarker] = []
self.imageMarkerWidgets: List[CoordinateSystemMarker] = []
self.trayMarkers: List[TrayMarker] = [] # in the new coord system
self.newTrayMarkers: List[TrayMarker] = [] # in the new coord system
self.layout = QtWidgets.QVBoxLayout()
self.setLayout(self.layout)
selectionLayout = QtWidgets.QHBoxLayout()
self.trayMarkersBtn: QtWidgets.QRadioButton = QtWidgets.QRadioButton('Use Tray Markers')
self.trayMarkersBtn.pressed.connect(self._useTrayMarkers)
self.trayMarkersBtn.setChecked(True)
self.imgMarkersBtn: QtWidgets.QRadioButton = QtWidgets.QRadioButton('Use Image Markers')
self.imgMarkersBtn.pressed.connect(self._useImageMarkers)
selectionLayout.addWidget(self.trayMarkersBtn)
selectionLayout.addWidget(self.imgMarkersBtn)
self.addMarkerBtn: QtWidgets.QPushButton = QtWidgets.QPushButton('Add New Markers')
self.addMarkerBtn.setStyleSheet("background-color : lightgrey")
self._formatAsToggleBtn(self.addMarkerBtn)
self.transferResult: QtWidgets.QLabel = QtWidgets.QLabel('No valid input')
self.trayMarkerGroup: QtWidgets.QGroupBox = self._getTrayMarkerGroup()
self.imgMarkerGroup: QtWidgets.QGroupBox = self._getImageMarkerGroup()
saveBtn: QtWidgets.QPushButton = QtWidgets.QPushButton('Save to Dataset')
saveBtn.clicked.connect(self._saveToDataset)
self.layout.addLayout(selectionLayout)
self.layout.addWidget(self.trayMarkerGroup)
self.layout.addWidget(self.transferResult)
self.layout.addWidget(saveBtn)
self._getMarkersFromDataset()
def _getMarkersFromDataset(self) -> None:
if self.viewParent is not None:
self.trayMarkers = deepcopy(self.viewParent.dataset.trayMarkers)
self.imageMarkers = deepcopy(self.viewParent.dataset.imageMarkers)
for index, imgMarker in enumerate(self.imageMarkers):
pxPos: tuple = (imgMarker.imgCoordX, imgMarker.imgCoordY)
newMarkerWidget: CoordinateSystemMarker = CoordinateSystemMarker(index, pxPos)
self.imageMarkerWidgets.append(newMarkerWidget)
self.viewParent.scene().addItem(newMarkerWidget)
def _formatAsToggleBtn(self, btn: QtWidgets.QPushButton) -> None:
btn.setCheckable(True)
btn.setChecked(False)
btn.clicked.connect(lambda: self._setBtnColor(btn))
def _getTrayMarkerGroup(self) -> QtWidgets.QGroupBox:
layout = QtWidgets.QGridLayout()
group: QtWidgets.QGroupBox = QtWidgets.QGroupBox('Sample Tray Markers')
group.setLayout(layout)
if len(self.trayMarkers) == 0:
layout.addWidget(QtWidgets.QLabel('No tray markers found.'))
for i in range(3):
layout.addWidget(QtWidgets.QLabel('New Marker Placeholder'))
return group
def _getImageMarkerGroup(self) -> QtWidgets.QGroupBox:
def makeCenterOnLambda(ind):
return lambda: self._centerOnImageMarker(ind)
def makeDeleteLambda(ind):
return lambda: self._deleteImageMarker(ind)
def makeReadNewPosLambda(ind):
return lambda: self._readNewImageMarker(ind)
layout = QtWidgets.QGridLayout()
group: QtWidgets.QGroupBox = QtWidgets.QGroupBox('Image Based Markers')
group.setLayout(layout)
layout.addWidget(self.addMarkerBtn)
if len(self.imageMarkers) == 0:
layout.addWidget(QtWidgets.QLabel('No image markers found.'))
else:
layout.addWidget(QtWidgets.QLabel('Number'), 1, 0)
layout.addWidget(QtWidgets.QLabel('Coordinates old'), 1, 1)
layout.addWidget(QtWidgets.QLabel('Coordinates new'), 1, 2)
for index, imgMarker in enumerate(self.imageMarkers):
# reset indices, as they could have been reordered by deleting a marker..
imgMarker.index = index
self.imageMarkerWidgets[index].index = index
newMarker: ImageMarker = self.newImageMarkers[index]
newMarker.index = index
newX, newY, newZ = newMarker.worldCoordX, newMarker.worldCoordY, newMarker.worldCoordZ
x, y, z = imgMarker.worldCoordX, imgMarker.worldCoordY, imgMarker.worldCoordZ
row: int = 2+index
updateBtn: QtWidgets.QPushButton = QtWidgets.QPushButton('Read Coordinates')
updateBtn.clicked.connect(makeReadNewPosLambda(index))
focusBtn: QtWidgets.QPushButton = QtWidgets.QPushButton('Center On')
focusBtn.clicked.connect(makeCenterOnLambda(index))
delBtn: QtWidgets.QPushButton = QtWidgets.QPushButton('Delete')
delBtn.clicked.connect(makeDeleteLambda(index))
layout.addWidget(QtWidgets.QLabel(str(imgMarker.index+1)), row, 0)
layout.addWidget(QtWidgets.QLabel(f'x: {round(x)} µm\ny: {round(y)} µm\nz: {round(z)} µm'), row, 1)
if np.nan in [newX, newY, newZ]:
layout.addWidget(QtWidgets.QLabel('Coordinates not yet read.'), row, 2)
else:
layout.addWidget(QtWidgets.QLabel(f'x: {round(newX)} µm\ny: {round(newY)} µm\nz: {round(newZ)} µm'), row, 2)
layout.addWidget(updateBtn, row, 3)
layout.addWidget(focusBtn, row, 4)
layout.addWidget(delBtn, row, 5)
return group
def _updateTransferResult(self) -> None:
oldMarkers: list = self.trayMarkers if self.trayMarkersBtn.isChecked() else self.imageMarkers
newMarkers: list = self.newTrayMarkers if self.trayMarkersBtn.isChecked() else self.newImageMarkers
srcPoints: np.ndarray = np.array(
[[marker.worldCoordX, marker.worldCoordY, marker.worldCoordZ] for marker in oldMarkers])
dstPoints: np.ndarray = np.array(
[[marker.worldCoordX, marker.worldCoordY, marker.worldCoordZ] for marker in newMarkers])
hasNan: bool = (np.any(np.isnan(srcPoints)) or np.any(np.isnan(dstPoints)))
if len(oldMarkers) == len(newMarkers) and len(oldMarkers) >= 3 and not hasNan:
transformMatrix, pc, zpc, residuals = getTransform(srcPoints, dstPoints)
self.transferResult.setText(f'Transform residuals (µm): {residuals}')
else:
self.transferResult.setText('No valid inputs for coordinate transfer')
def _setBtnColor(self, btn: QtWidgets.QPushButton):
"""
Sets color of the toggle button to indicate its status.
"""
if btn.isChecked():
btn.setStyleSheet("background-color : lightblue")
else:
btn.setStyleSheet("background-color : lightgrey")
def _useTrayMarkers(self) -> None:
"""
Use markers on the sample tray that are NOT in the microscope image.
"""
self.imgMarkerGroup.setParent(None)
self.trayMarkerGroup.setParent(None)
self.trayMarkerGroup = self._getTrayMarkerGroup()
self.layout.insertWidget(1, self.trayMarkerGroup)
def _useImageMarkers(self) -> None:
"""
Use markers that are defined through characteristic spots within the microscope image.
"""
self.imgMarkerGroup.setParent(None)
self.trayMarkerGroup.setParent(None)
self.imgMarkerGroup = self._getImageMarkerGroup()
self.layout.insertWidget(1, self.imgMarkerGroup)
self._updateTransferResult()
def mousePressEvent(self, event: QtGui.QMouseEvent) -> None:
if self.addMarkerBtn.isChecked() and event.button() == QtCore.Qt.LeftButton:
scenePos = self.viewParent.mapToScene(event.pos())
self._addNewImageMarker((scenePos.x(), scenePos.y()))
def _deleteImageMarker(self, markerIndex: int) -> None:
self.imageMarkers.remove(self.imageMarkers[markerIndex])
self.newImageMarkers.remove(self.newImageMarkers[markerIndex])
self.viewParent.scene().removeItem(self.imageMarkerWidgets[markerIndex])
self.imageMarkerWidgets.remove(self.imageMarkerWidgets[markerIndex])
self._useImageMarkers()
def _centerOnImageMarker(self, markerIndex: int) -> None:
self.viewParent.centerOn(self.imageMarkerWidgets[markerIndex])
def _addNewImageMarker(self, pos: tuple) -> None:
newImageMarker: ImageMarker = ImageMarker()
newImageMarker.index = len(self.imageMarkers)
x, y, z = self.ramanctrl.getPosition()
newImageMarker.worldCoordX = x
newImageMarker.worldCoordY = y
newImageMarker.worldCoordZ = z
newImageMarker.imgCoordX = pos[0]
newImageMarker.imgCoordY = pos[1]
self.imageMarkers.append(newImageMarker)
newNewImageMarker: ImageMarker = ImageMarker()
newNewImageMarker.imgCoordX = pos[0]
newNewImageMarker.imgCoordY = pos[1]
self.newImageMarkers.append(newNewImageMarker)
newMarkerWidget: CoordinateSystemMarker = CoordinateSystemMarker(len(self.imageMarkers), pos)
self.imageMarkerWidgets.append(newMarkerWidget)
self.viewParent.scene().addItem(newMarkerWidget)
self._useImageMarkers()
def _readNewImageMarker(self, index: int) -> None:
"""Reads current instrument coordinates and assignes them to the respective "new image marker" """
x, y, z = self.ramanctrl.getPosition()
self.newImageMarkers[index].worldCoordX = x
self.newImageMarkers[index].worldCoordY = y
self.newImageMarkers[index].worldCoordZ = z
self._useImageMarkers()
def _saveToDataset(self) -> None:
if self.trayMarkersBtn.isChecked():
print('saving tray markers to dataset')
else:
print('saving image makers to dataset')
def closeEvent(self, a0: QtGui.QCloseEvent) -> None:
reply = QtWidgets.QMessageBox.question(self, 'Close without saving',
'The window is about to be closed.\nSave markers prior to closing?',
QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No,
QtWidgets.QMessageBox.Yes)
if reply == QtWidgets.QMessageBox.Yes:
self._saveToDataset()
if self.viewParent is not None:
self.viewParent.showHiddenWidgets()
self.viewParent.coordTransferWidget = None
del self
class CoordinateSystemMarker(QtWidgets.QGraphicsItem):
def __init__(self, index: int, position: tuple):
super().__init__()
self.setPos(position[0], position[1])
self.setFlag(QtWidgets.QGraphicsItem.ItemIsMovable)
self.setCacheMode(QtWidgets.QGraphicsItem.DeviceCoordinateCache)
self.index = index
self.pxSize: int = 101
self.gapSize: int = 10
# self.setFlag(QtWidgets.QGraphicsItem.ItemSendsGeometryChanges)
# self.poschanged = False
def boundingRect(self) -> QtCore.QRectF:
return QtCore.QRectF(-self.pxSize/2, -self.pxSize/2, self.pxSize, self.pxSize)
def paint(self, painter: QtGui.QPainter, option, widget) -> None:
halfSize: int = int(round(self.pxSize / 2))
halfGapSize: int = int(round(self.gapSize / 2))
painter.setPen(QtCore.Qt.green)
painter.setBrush(QtGui.QColor(30, 255, 30, 64))
painter.drawEllipse(-halfSize, -halfSize, self.pxSize, self.pxSize)
# horizontal lines
painter.drawLine(-halfSize, 0, -halfGapSize, 0)
painter.drawLine(halfGapSize, 0, halfSize, 0)
# vertical lines
painter.drawLine(0, -halfSize, 0, -halfGapSize)
painter.drawLine(0, halfGapSize, 0, halfSize)
painter.drawText(-halfSize, -halfSize, str(f'Marker {self.index+1}'))
if __name__ == '__main__':
import sys
app = QtWidgets.QApplication(sys.argv)
coordUI = CoordTransformUI(None)
coordUI.show()
ret = app.exec_()
helperfunctions.py
View file @ 34439505
......@@ -30,6 +30,9 @@ except ImportError:
skimread = None
skimsave = None
from .ramancom.ramanbase import RamanBase
from logging import Logger
def cv2imread_fix(fname, flags=cv2.IMREAD_COLOR):
if skimread is not None:
return skimread(fname, as_gray=(flags==cv2.IMREAD_GRAYSCALE))
......@@ -95,4 +98,15 @@ def polygoncovering(boundary, wx, wy):
poslist.extend([[xi,yi+.5*wy] for xi in (x if i%2==0 else x[::-1])])
x0clast, x1clast = x0c, x1c
return poslist
\ No newline at end of file
def getRamanControl(controlclass: RamanBase, logger: Logger) -> RamanBase:
simulatedInterface: bool = False
if 'simulatedInterface' in controlclass.__dict__.keys():
if controlclass.__dict__['simulatedInterface'] == True:
simulatedInterface = True
if simulatedInterface:
ramanctrl = controlclass(logger, ui=False)
else:
ramanctrl = controlclass(logger)
return ramanctrl
opticalbackground.py
View file @ 34439505
......@@ -133,7 +133,7 @@ class BackGroundManager(QtWidgets.QWidget):
if img is not None:
prevImg = img
else:
prevImg = np.zeros((300, 300))
prevImg = np.zeros((300, 300, 3))
if convertColors:
prevImg = cv2.cvtColor(img, cv2.COLOR_RGB2BGR)
......
opticalscan.py
View file @ 34439505
......@@ -23,12 +23,13 @@ from PyQt5 import QtCore, QtWidgets
import numpy as np
from multiprocessing import Process, Queue, Event
import queue
from .imagestitch import imageStacking
import os, sys
import os
import logging
import logging.handlers
import cv2
from .helperfunctions import cv2imread_fix, cv2imwrite_fix
from typing import List
from .imagestitch import imageStacking
from .helperfunctions import cv2imread_fix, cv2imwrite_fix, getRamanControl
from time import time, localtime, strftime
from .opticalbackground import BackGroundManager
from .uielements import TimeEstimateProgressbar
......@@ -51,7 +52,7 @@ def scan(path, sol, zpositions, grid, controlclass, dataqueue,
logger.info('starting new optical scan')
try:
ramanctrl = controlclass(logger)
ramanctrl = getRamanControl(controlclass, logger)
ramanctrl.connect()
zlist = list(enumerate(zpositions))
for i, p in enumerate(grid):
......@@ -135,8 +136,8 @@ def removeSrcTiles(names, path):
os.remove(fpath)
def loadAndPasteImage(srcnames, pyramid, fullzval, width, height,
rotationvalue, p0, p1, p, logger, background=None):
def loadAndPasteImage(srcnames: List[str], pyramid, fullzval: np.ndarray, width: float, height: float,
rotationvalue: float, p0: List[float], p1: List[float], p: List[float], logger, background=None):
"""
:param list of str srcnames: list of stacked scan files to merge
:param ScenePyramid pyramid: the scene pyramid
......@@ -147,6 +148,7 @@ def loadAndPasteImage(srcnames, pyramid, fullzval, width, height,
:param list of float p0: (min x; max y) of scan tile positions
:param list of float p1: (max x; min y) of scan tile positions
:param list of float p: position of current scan tile
:param logger: the logger to use
:param numpy.ndarray background:
:return:
"""
......@@ -193,6 +195,7 @@ class PointCoordinates(QtWidgets.QGridLayout):
def __init__(self, N, ramanctrl, parent=None, names=None):
super().__init__(parent)
self.validpoints = [False]*N
self.dswidgets = []
self.N = 0
self.ramanctrl = ramanctrl
......@@ -204,20 +207,20 @@ class PointCoordinates(QtWidgets.QGridLayout):
@QtCore.pyqtSlot()
def createWidgets(self, N, pointsgiven=[]):
self.validpoints = [False]*N
points = np.zeros((N,3))
points = np.zeros((N, 3))
def connect(button, index):
button.released.connect(QtCore.pyqtSlot()(lambda : self.read(index)))
button.released.connect(QtCore.pyqtSlot()(lambda: self.read(index)))
for i in range(self.N,min(N,len(self.dswidgets))):
self.itemAtPosition(i+1,0).setVisible(True)
self.itemAtPosition(i+1,1).setVisible(True)
self.itemAtPosition(i+1,2).setVisible(True)
self.itemAtPosition(i+1,3).setVisible(True)
self.itemAtPosition(i+1,4).setVisible(True)
self.itemAtPosition(i+1,5).setVisible(True)
self.itemAtPosition(i+1,6).setVisible(True)
for i in range(self.N, min(N, len(self.dswidgets))):
self.itemAtPosition(i+1, 0).setVisible(True)
self.itemAtPosition(i+1, 1).setVisible(True)
self.itemAtPosition(i+1, 2).setVisible(True)
self.itemAtPosition(i+1, 3).setVisible(True)
self.itemAtPosition(i+1, 4).setVisible(True)
self.itemAtPosition(i+1, 5).setVisible(True)
self.itemAtPosition(i+1, 6).setVisible(True)
for i in range(self.N, N):
if self.names is not None:
lx = QtWidgets.QLabel(f"{self.names[i]} -> x:")
......@@ -228,15 +231,12 @@ class PointCoordinates(QtWidgets.QGridLayout):
wx = QtWidgets.QDoubleSpinBox()
wy = QtWidgets.QDoubleSpinBox()
wz = QtWidgets.QDoubleSpinBox()
wx.setDecimals(1)
wy.setDecimals(1)
wz.setDecimals(1)
wx.setRange(-500_000, 500_000)
wy.setRange(-500_000, 500_000)
wz.setRange(-500_000, 500_000)
wx.setValue(points[i,0])
wy.setValue(points[i,1])
wz.setValue(points[i,2])
for index, spinbox in enumerate([wx, wy, wz]):
spinbox.setDecimals(1)
spinbox.setRange(-500_000, 500_000)
spinbox.setValue(points[i, index])
spinbox.setMaximumWidth(75)
self.addWidget(lx, i+1, 0, QtCore.Qt.AlignLeft)
self.addWidget(wx, i+1, 1, QtCore.Qt.AlignRight)
self.addWidget(ly, i+1, 2, QtCore.Qt.AlignLeft)
......@@ -247,15 +247,15 @@ class PointCoordinates(QtWidgets.QGridLayout):
connect(pread, i)
self.addWidget(pread, i+1, 6, QtCore.Qt.AlignRight)