added collector functions to simplify workflows

LaueTools/imagescollector.py

@@ -0,0 +1,140 @@
+# -*- coding: utf-8 -*-
+r"""
+imagescollector module is made for reading data contained in binary image file
+fully or partially.
+
+"""
+__author__ = "Jean-Sebastien Micha, CRG-IF BM32 @ ESRF"
+
+# built-in modules
+import os
+
+import LaueTools.generaltools as GT
+import LaueTools.IOimagefile as IOimage  
+import LaueTools.readmccd as RMCCD
+
+
+def collectpixelvalue_singlefile(index, peaklist=None, prefix=None, folder =None,CCDLabel='sCMOS'):
+    """ collect single pixel intensities located in several locations (defined by peaklist) in 1 image
+    
+    :param index: int, image file index 
+    :param peaklist: list or array of 2d pixels position
+    :param prefix: str, prefix of imagefilename (excluding folder path) excluding digits number of the index
+    ('Cu_' for images named  'Cu_0020.tif')
+    :param CCDLabel: label of detector
+    
+    :return: array of pixel values with shape = (nbimages, nbpeaks)
+
+    """
+    filename = prefix+'%04d'%index + '.tif'   
+    imagefilename = os.path.join(folder, filename)
+
+    pixvals = IOimage.pixelvalat(imagefilename, xy=peaklist, sortpeaks=False, CCDLabel=CCDLabel)
+    return pixvals
+
+
+
+def collectroismax_singlefile(index, roicenters=None, prefix=None, folder =None,
+                            boxsize_row=10,boxsize_line=10,CCDLabel=None):
+    """ collect max intensity in some given rois centered on peaks defined in peaklist in 1 image
+    
+    
+        
+    :param index: int, image file index
+    :param roicenters: list or array of 2d PIXELS position
+    :param prefix: str, prefix of imagefilename (excluding folder path) excluding digits number of the index
+    ('Cu_' for images named  'Cu_0020.tif')
+    :param folder: str, path to folder containing all images
+    :param boxsize_row, boxsize_line: half boxsize along x and y of the roi (can be a list?)
+    :param CCDLabel: label of detector
+    
+    :return: array of max intensities: shape = (nbimages, nbpeaks)
+    """
+    filename = prefix+'%04d'%index + '.tif'   
+    imagefilename = os.path.join(folder, filename)
+
+    pixvals = IOimage.getroismax(imagefilename, roicenters=roicenters,
+                                 halfboxsize=(boxsize_row,boxsize_line), CCDLabel=CCDLabel)
+    return pixvals
+
+def collectroisXYmax_singlefile(index, roicenters=None, prefix=None, folder =None,
+                            boxsize_row=10,boxsize_line=10,CCDLabel=None):
+    """ collect pixel XY position of max intensity in some given rois centered on peaks defined in peaklist in 1 image
+
+    :param index: int, image file index
+    :param peaklist: list or array of 2d pixels position
+    :param prefix: str, prefix of imagefilename (excluding folder path) excluding digits number of the index
+    ('Cu_' for images named  'Cu_0020.tif')
+    :param folder: str, path to folder containing all images
+    :param boxsize_row, boxsize_line: half boxsize along x and y of the roi (can be a list?)
+    :param CCDLabel: label of detector
+    
+    :return: array of max intensities: shape = (nbimages, nbpeaks)
+    """
+    filename = prefix+'%04d'%index + '.tif'   
+    imagefilename = os.path.join(folder, filename)
+
+    pixvals = IOimage.getroisXYmax(imagefilename, roicenters=roicenters,
+                                   halfboxsize=(boxsize_row,boxsize_line),
+                                   CCDLabel=CCDLabel)
+    return pixvals
+
+def collectroisXYcenterofmass_singlefile(index, roicenters=None, prefix=None, folder =None,
+                            boxsize_row=10,boxsize_line=10,CCDLabel=None):
+    """ collect pixel XY position of max intensity in some given rois centered on peaks defined in peaklist in 1 image
+
+    :param index: int, image file index
+    :param peaklist: list or array of 2d pixels position
+    :param prefix: str, prefix of imagefilename (excluding folder path) excluding digits number of the index
+    ('Cu_' for images named  'Cu_0020.tif')
+    :param folder: str, path to folder containing all images
+    :param boxsize_row, boxsize_line: half boxsize along x and y of the roi (can be a list?)
+    :param CCDLabel: label of detector
+    
+    :return: array of max intensities: shape = (nbimages, nbpeaks)
+    """
+    filename = prefix+'%04d'%index + '.tif'   
+    imagefilename = os.path.join(folder, filename)
+
+    pixvals = IOimage.getroiscenterofmass(imagefilename, roicenters=roicenters,
+                                   halfboxsize=(boxsize_row,boxsize_line),
+                                   CCDLabel=CCDLabel)
+    return pixvals
+
+def collectroisfitpeak_singlefile(index, roicenters=None, prefix=None,
+                                  folder =None,
+                            boxsize_row=10,boxsize_line=10,CCDLabel=None):
+    """ collect pixel XY position of max intensity in some given rois centered on peaks defined in peaklist in 1 image
+
+    :param index: int, image file index
+    :param peaklist: list or array of 2d pixels position
+    :param prefix: str, prefix of imagefilename (excluding folder path) excluding digits number of the index
+    ('Cu_' for images named  'Cu_0020.tif')
+    :param folder: str, path to folder containing all images
+    :param boxsize_row, boxsize_line: half boxsize along x and y of the roi (can be a list?)
+    :param CCDLabel: label of detector
+    
+    :return: array of max intensities: shape = (nbimages, nbpeaks)
+    """
+    filename = prefix+'%04d'%index + '.tif'   
+    imagefilename = os.path.join(folder, filename)
+
+    resfit = RMCCD.readoneimage_multiROIfit(imagefilename,
+                                        roicenters,
+                                        [boxsize_row,boxsize_line],
+                                        stackimageindex=-1,
+                                        CCDLabel=CCDLabel,
+                                        baseline="auto",  # min in ROI box
+                                        startangles=0.0,
+                                        start_sigma1=1.,
+                                        start_sigma2=1.,
+                                        position_start='max',  # 'centers' or 'max'
+                                        showfitresults=0,
+                                        offsetposition=1,
+                                        fitfunc="gaussian",
+                                        xtol=0.00001,
+                                        addImax=False,
+                                        use_data_corrected=None)
+    #  bkg, amp, x, y std1, std2, angle
+    #print('resfit',resfit)
+    return resfit[0]