orGUI 1.0.1__py3-none-any.whl

orgui/backend/beamline/P212_tools.py

@@ -0,0 +1,577 @@
+# -*- coding: utf-8 -*-
+# /*##########################################################################
+#
+# Copyright (c) 2020-2024 Timo Fuchs
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+__author__ = "Timo Fuchs"
+__copyright__ = "Copyright 2020-2024 Timo Fuchs"
+__license__ = "MIT License"
+__version__ = "1.0.0"
+__maintainer__ = "Timo Fuchs"
+__email__ = "fuchs@physik.uni-kiel.de"
+
+
+import numpy as np
+import scipy.ndimage
+import scipy.interpolate
+import scipy.optimize
+from matplotlib.colors import LinearSegmentedColormap
+import datetime
+import re
+sqrt3 = np.sqrt(3)
+import warnings
+import fabio
+import h5py
+import os
+import re
+from datetime import datetime
+from .fio_reader import FioFile
+#from fio_reader import FioFile
+import silx.io
+from silx.io import dictdump
+
+# not in use!!!
+class P3_Image:
+    def __init__(self, filename,edf=False):
+        if edf:
+            image = fabio.open(filename)
+            #edf = EdfFile.EdfFile(filename, 'r')
+            #self.header = edf.GetHeader(0)
+            self.header = image.header
+            #self.header = edf.GetHeader(0)
+            self.motors = dict()
+            motor_mne = self.header['motor_mne'].split()
+            motor_pos = self.header['motor_pos'].split()
+            for i in range(len(motor_mne)):
+                self.motors[motor_mne[i]] = float(motor_pos[i])
+            self.counters = dict()
+            counter_mne = self.header['counter_mne'].split()
+            counter_pos = self.header['counter_pos'].split()
+            for i in range(len(counter_mne)):
+                self.counters[counter_mne[i]] = float(counter_pos[i])
+            self.img = image.data.astype(np.float64)
+            #self.img = np.array(edf.GetData(0), dtype=float)
+        else:
+            try:
+                image = fabio.open(filename)
+                self.header = image.header
+                self.img = image.data.astype(np.float64)
+            except Exception as e:
+                warnings.warn("Cannot open image, ok only during test run!!! %s" % e)
+                self.header = ""
+                #self.img = np.zeros((2880, 2880))
+
+
+            
+
+            self.motors = dict() # not available in cbf
+            self.counters = dict() # not available in cbf
+
+            
+
+
+class PE_Image:
+    def __init__(self, filename, dark=None):
+        
+        with fabio.open(filename) as img:
+            self.img = img.data.astype(np.float64)
+            self.header = img.header
+        self.motors = dict() # not jet available
+        self.counters = dict() # not jet available
+        if dark is not None:
+            self.img -= dark
+            # crude repair of images
+            #if np.mean(self.img) < 0:
+            #    self.img += 72.2
+        self.img = np.fliplr(self.img.T)
+
+class H5Fastsweep(object):
+    def __init__(self, hdffilepath_orNode=None, scanno=None):
+    
+
+        #self.scanname = scanname
+        self.cameras = []
+        data = None
+        
+        if hdffilepath_orNode is None:
+            return
+        self.hdffilepath_orNode=hdffilepath_orNode    
+
+        if isinstance(hdffilepath_orNode, str):
+            self.hdffilepath_orNode = os.path.abspath(hdffilepath_orNode)
+            filepath,filename = os.path.split(self.hdffilepath_orNode)
+            filename_noext,_ = os.path.splitext(filepath)
+            #filename_noext = filename.split('.')[0]
+            self.filename_base = filename_noext #filename_noext[:filename_noext.rfind('_')]
+            with silx.io.open(self.hdffilepath_orNode) as f:
+                #print([d for d in f])
+                for d in f:
+                    scanno_s, subscanno = d.split('.')
+                    if int(scanno_s) == scanno:
+                        break
+                else:
+                    raise IOError("Scan number %s not found in file" % scanno)
+                self.scanname = '.'.join((scanno_s,subscanno))
+
+                data = dictdump.h5todict(f,self.scanname)
+                
+                    
+        else:
+            hdffilepath = hdffilepath_orNode.local_filename
+            filepath,filename = os.path.split(hdffilepath)
+            filename_noext,_ = os.path.splitext(filepath)
+            self.filename_base = filename_noext
+            
+            f = hdffilepath_orNode.file
+            for d in f:
+                scanno_s, subscanno = d.split('.')
+                if int(scanno_s) == scanno:
+                    break
+            else:
+                raise IOError("Scan number %s not found in file" % scanno)
+            self.scanname = '.'.join((scanno_s,subscanno))
+
+            data = dictdump.h5todict(f,self.scanname)
+    
+        self.th = data['measurement']['idrz1(encoder)']
+        dth = np.mean(np.diff(self.th))
+        self.th += dth
+        self.th = self.th[1:-1] #last image is missing, first image is dark file
+        
+        self.th -= 180.
+        
+        #meandt = np.mean(np.diff(datafile.data['time']))
+        self.exposure_time = np.full_like(self.th,1.) #np.diff(datafile.data['time'],append=(datafile.data['time'][-1] + meandt))
+        self.time = data['measurement']['time'][1:-1]
+        #self.th = -1*self.th  # orientation of th is inversed
+        self.omega = -1*self.th
+        
+        
+        
+        #self.exposure_time = np.full_like(self.th,self.exposure_time)
+        self.directFolder = True
+        self.imagenames = data['measurement']['filename']
+        #from IPython import embed; embed()
+        parsedscanname = re.compile('=\"([^\"]*)\"').findall(str(data['title']))
+        
+        directory = parsedscanname[1]
+        _,folder = os.path.split(directory)
+        imagefolder = os.path.join(os.path.split(filepath)[0],folder)
+        
+        self.filenames = [os.path.join(imagefolder,imgname) for imgname in self.imagenames ]
+        with fabio.open(self.filenames[0]) as fiof:
+            self.dark = fiof.data
+        
+        self.filenames = self.filenames[1:-1]
+        #self.set_image_folder(self.path+ "/" + detector )
+        self.nopoints = self.th.size
+        self.axisname = 'th'
+        self.axis = getattr(self,self.axisname)
+   
+
+        
+    def set_th_offset(self,offset):
+        self.th += offset
+        self.omega = -1*self.th
+
+    """
+    def set_image_folder(self,path_to_folder):
+        #self.filenames = [None]*len(self.th)
+        self.filenames = []
+        basefolder = path_to_folder.split('/')[-1]
+        self.imageprefix = basefolder.split('_')[0]
+        if self.directFolder:
+            for i in range(self.th.size):
+                self.filenames.append("%s/%s_%05i.%s" % (path_to_folder,\
+                    self.imageprefix,i+self.first_imageno,self.imagesuffix))
+        else:
+            for i in range(self.th.size):
+                self.filenames.append("%s/%s/%s_%05.cbf" % (path_to_folder,\
+                    self.filename_base,self.filename_base,self.first_imageno+i))
+    """        
+    def get_raw_P3_img(self,img):
+        return PE_Image(self.filenames[img],self.dark)
+        
+    # returns single default image!
+    def get_raw_img(self,img):
+        return PE_Image(self.filenames[img],self.dark)
+    
+    def get_P3_img(self,img):
+        imgdata = PE_Image(self.filenames[img],self.dark)
+        imgdata.counters['Time'] = self.time[img]
+        imgdata.counters['TrigTime'] = self.exposure_time[img]
+        imgdata.counters['th'] = self.th[img]
+        imgdata.counters['om'] = self.omega[img]
+        if self.current is not None:
+            imgdata.counters['srcur'] = self.current[img]
+        return imgdata
+    
+    def __getitem__(self,key):
+        return self.get_P3_img(key)
+    
+    def __len__(self):
+        return self.nopoints
+
+
+# only log file existing
+class XRRScan(object):
+    def __init__(self,logfilepath,img_prefix="xx",scanno=None):
+        self.path,fname = os.path.split(logfilepath)
+        #fnamewotsuff, suffix = fname.split('.')
+        #prefix, nostr = fnamewotsuff.split('_')
+        #if scanno is None:
+        #    scanno = int(nostr)
+        #fiofilecorrectedscanno = "%s/%s_%05i.%s" % (self.path,prefix,scanno,suffix) 
+        #self.dtime = []
+        #self.current = [] # sr current or some other monitor is missing!
+        with open(logfilepath,'r') as logfile:
+            line = logfile.readline()
+            self.header = []
+            while line.startswith('#'): # in header
+                self.header.append(line.strip('#').strip())
+                lineno = logfile.tell()
+                line = logfile.readline()
+            logfile.seek(lineno)
+            data = np.genfromtxt(logfile)
+        self.mu = -1*data[:,1]
+        self.th = np.full_like( self.mu,float( self.header[4].split()[-1] ))
+            
+        
+        #datafile = FioFile(fiofilecorrectedscanno)
+        #self.th = datafile.data['idrz1']
+        # ********** temporary fix *************************************
+        self.th -= 80.0
+        # **************************************************************
+        #imgfilepath, img_foldername = os.path.split(img_prefix)
+        #imagefoldernumber = int(img_foldername.split('_')[0])
+        #voltagelog = np.genfromtxt("%s/%i_voltage.log" % (imgfilepath,imagefoldernumber))
+        # file not saved !!! shit!
+        
+        #meandt = np.mean(np.diff(datafile.data['time']))
+        
+        self.exposure_time = np.full_like( self.mu,0.5) # for all XRRs in Dec 2019 beamtime
+        
+        self.time = data[:,0]
+        #self.th = -1*self.th  # orientation of th is inversed
+        self.omega = -1*self.th
+        self.current = data[:,2]
+        
+        
+        #self.exposure_time = np.full_like(self.th,self.exposure_time)
+        self.directFolder = True
+        #self.imagenames = datafile.data['filename']
+
+        self.imageprefix,fmiddle = img_prefix, "00001.tif"
+        self.imagesuffix = fmiddle.split('.')[-1]
+        self.first_imageno = 1
+        
+        #self.set_image_folder(self.path+ "/" + detector )
+        self.nopoints = self.th.size
+        
+        self.set_image_folder(img_prefix)
+
+    def set_th_offset(self,offset):
+        self.th += offset
+        self.omega = -1*self.th
+        
+    def set_image_folder(self,path_to_folder):
+        #self.filenames = [None]*len(self.th)
+        self.filenames = []
+        basefolder = path_to_folder.split('/')[-1]
+        self.imageprefix = basefolder.split('_')[0]
+        if self.directFolder:
+            for i in range(self.th.size):
+                self.filenames.append("%s/%s_%05i.%s" % (path_to_folder,\
+                    self.imageprefix,i+self.first_imageno,self.imagesuffix))
+        else:
+            for i in range(self.th.size):
+                self.filenames.append("%s/%s/%s_%05.cbf" % (path_to_folder,\
+                    self.filename_base,self.filename_base,self.first_imageno+i))
+            
+    def get_raw_P3_img(self,img):
+        return P3_Image(self.filenames[img])
+        
+    # returns single default image!
+    def get_raw_img(self,img):
+        return P3_Image(self.filenames[img])
+    
+    def get_P3_img(self,img):
+        imgdata = P3_Image(self.filenames[img])
+        imgdata.counters['Time'] = self.time[img]
+        imgdata.counters['TrigTime'] = self.exposure_time[img]
+        imgdata.counters['th'] = self.th[img]
+        imgdata.counters['om'] = self.omega[img]
+        if self.current is not None:
+            imgdata.counters['srcur'] = self.current[img]
+        if self.mu is not None:
+            imgdata.counters['mu'] = self.mu[img]
+        return imgdata
+    
+    def __getitem__(self,key):
+        return self.get_P3_img(key)
+    
+    def __len__(self):
+        return self.nopoints    
+
+      
+class FioFastsweep(object):
+    def __init__(self,fiofilepath,img_prefix="xx",scanno=None):
+        self.path,fname = os.path.split(fiofilepath)
+        fnamewotsuff, suffix = fname.split('.')
+        prefix, nostr = fnamewotsuff.split('_')
+        if scanno is None:
+            scanno = int(nostr)
+        fiofilecorrectedscanno = "%s/%s_%05i.%s" % (self.path,prefix,scanno,suffix) 
+        #self.dtime = []
+        #self.current = [] # sr current or some other monitor is missing!
+        datafile = FioFile(fiofilecorrectedscanno)
+        self.th = datafile.data['idrz1']
+        # ********** temporary fix *************************************
+        self.th -= 80.0
+        # **************************************************************
+        #imgfilepath, img_foldername = os.path.split(img_prefix)
+        #imagefoldernumber = int(img_foldername.split('_')[0])
+        #voltagelog = np.genfromtxt("%s/%i_voltage.log" % (imgfilepath,imagefoldernumber))
+        # file not saved !!! shit!
+        
+        meandt = np.mean(np.diff(datafile.data['time']))
+        self.exposure_time = np.diff(datafile.data['time'],append=(datafile.data['time'][-1] + meandt))
+        self.time = datafile.data['time']
+        #self.th = -1*self.th  # orientation of th is inversed
+        self.omega = -1*self.th
+        
+        
+        
+        #self.exposure_time = np.full_like(self.th,self.exposure_time)
+        self.directFolder = True
+        self.imagenames = datafile.data['filename']
+        try:
+            self.imageprefix,fmiddle = self.imagenames[0].split('_')
+            self.imagesuffix = fmiddle.split('.')[-1]
+            print(self.imageprefix)
+        except:
+            self.imageprefix,fmiddle = img_prefix, "00001.tif"
+            self.imagesuffix = fmiddle.split('.')[-1]
+        self.first_imageno = 1
+        self.current = None
+        #self.set_image_folder(self.path+ "/" + detector )
+        self.nopoints = self.th.size
+        
+        
+   
+
+        
+    def set_th_offset(self,offset):
+        self.th += offset
+        self.omega = -1*self.th
+
+        
+    def set_image_folder(self,path_to_folder):
+        #self.filenames = [None]*len(self.th)
+        self.filenames = []
+        basefolder = path_to_folder.split('/')[-1]
+        self.imageprefix = basefolder.split('_')[0]
+        if self.directFolder:
+            for i in range(self.th.size):
+                self.filenames.append("%s/%s_%05i.%s" % (path_to_folder,\
+                    self.imageprefix,i+self.first_imageno,self.imagesuffix))
+        else:
+            for i in range(self.th.size):
+                self.filenames.append("%s/%s/%s_%05.cbf" % (path_to_folder,\
+                    self.filename_base,self.filename_base,self.first_imageno+i))
+            
+    def get_raw_P3_img(self,img):
+        return P3_Image(self.filenames[img])
+        
+    # returns single default image!
+    def get_raw_img(self,img):
+        return P3_Image(self.filenames[img])
+    
+    def get_P3_img(self,img):
+        imgdata = P3_Image(self.filenames[img])
+        imgdata.counters['Time'] = self.time[img]
+        imgdata.counters['TrigTime'] = self.exposure_time[img]
+        imgdata.counters['th'] = self.th[img]
+        imgdata.counters['om'] = self.omega[img]
+        if self.current is not None:
+            imgdata.counters['srcur'] = self.current[img]
+        return imgdata
+    
+    def __getitem__(self,key):
+        return self.get_P3_img(key)
+    
+    def __len__(self):
+        return self.nopoints
+        
+class FioFastsweep_original(object):
+    def __init__(self,fiofilepath,scanno=None):
+        self.path,fname = os.path.split(fiofilepath)
+        fnamewotsuff, suffix = fname.split('.')
+        prefix, nostr = fnamewotsuff.split('_')
+        if scanno is None:
+            scanno = int(nostr)
+        fiofilecorrectedscanno = "%s/%s_%05i.%s" % (self.path,prefix,scanno,suffix) 
+        #self.dtime = []
+        #self.current = [] # sr current or some other monitor is missing!
+        datafile = FioFile(fiofilecorrectedscanno)
+        self.th = datafile.data['idrz1']
+        meandt = np.mean(np.diff(datafile.data['time']))
+        self.exposure_time = np.diff(datafile.data['time'],append=(datafile.data['time'][-1] + meandt))
+        self.time = datafile.data['time']
+        #self.th = -1*self.th  # orientation of th is inversed
+        self.omega = -1*self.th
+        #self.exposure_time = np.full_like(self.th,self.exposure_time)
+        self.directFolder = True
+        self.imagenames = datafile.data['filename']
+        print(self.imagenames)
+        self.imageprefix,fmiddle = self.imagenames[0].split('_')
+        self.imagesuffix = fmiddle.split('.')[-1]
+        self.first_imageno = 1
+        self.current = None
+        #self.set_image_folder(self.path+ "/" + detector )
+        self.nopoints = self.th.size
+            
+
+        
+    def set_th_offset(self,offset):
+        self.th += offset
+        self.omega = -1*self.th
+
+        
+    def set_image_folder(self,path_to_folder):
+        #self.filenames = [None]*len(self.th)
+        self.filenames = []
+        if self.directFolder:
+            for i in range(self.th.size):
+                self.filenames.append("%s/%s_%05i.%s" % (path_to_folder,\
+                    self.imageprefix,i+self.first_imageno,self.imagesuffix))
+        else:
+            for i in range(self.th.size):
+                self.filenames.append("%s/%s/%s_%05.cbf" % (path_to_folder,\
+                    self.filename_base,self.filename_base,self.first_imageno+i))
+            
+    def get_raw_P3_img(self,img):
+        return P3_Image(self.filenames[img])
+        
+    # returns single default image!
+    def get_raw_img(self,img):
+        return P3_Image(self.filenames[img])
+    
+    def get_P3_img(self,img):
+        imgdata = P3_Image(self.filenames[img])
+        imgdata.counters['Time'] = self.time[img]
+        imgdata.counters['TrigTime'] = self.exposure_time[img]
+        imgdata.counters['th'] = self.th[img]
+        imgdata.counters['om'] = self.omega[img]
+        if self.current is not None:
+            imgdata.counters['srcur'] = self.current[img]
+        return imgdata
+    
+    def __getitem__(self,key):
+        return self.get_P3_img(key)
+    
+    def __len__(self):
+        return self.nopoints
+            
+    
+        
+        
+class CrudeThScan(object):
+    def __init__(self,logfilepath,detector='PE1',darkfile=None):
+        self.path,_ = os.path.split(logfilepath)
+        self.th = []
+        self.dtime = []
+        self.current = []
+        self.dark = None
+        with open(logfilepath,'r') as f:
+            for l in f:
+                if l.startswith('#'):
+                    if 'Exposure time' in l:
+                        lsp = l.split()
+                        self.exposure_time = float(lsp[2][:-1])
+                    continue
+                lspl = l.split()
+                self.th.append(float(lspl[0]))
+                self.current.append(float(lspl[2]))
+                self.dtime.append(datetime.strptime(lspl[3] + ' ' + lspl[4],"%Y-%m-%d %H:%M:%S.%f"))
+            self.th = np.array(self.th)
+            self.current = np.array(self.current)
+            self.time = []
+            for t in self.dtime:
+                self.time.append(t.day*24*3600 + t.hour*3600 + t.minute*60 + t.second + t.microsecond*1e-6)
+            self.time = np.array(self.time)
+        #self.th = -1*self.th  # orientation of th is inversed
+        self.omega = -1*self.th
+        self.exposure_time = np.full_like(self.th,self.exposure_time)
+        self.directFolder = True
+        self.filename_base = 'pe'
+        self.first_imageno = 1
+        self.set_image_folder(self.path+ "/" + detector )
+        self.nopoints = self.th.size
+        
+        if darkfile is not None:
+            with fabio.open(darkfile) as img:
+                self.dark = img.data.astype(np.float64)
+            
+
+        
+    def set_th_offset(self,offset):
+        self.th += offset
+        self.omega = -1*self.th
+
+        
+    def set_image_folder(self,path_to_folder):
+        #self.filenames = [None]*len(self.th)
+        self.filenames = []
+        if self.directFolder:
+            for i in range(self.th.size):
+                self.filenames.append("%s/%s%05i.tif.gz" % (path_to_folder,\
+                    self.filename_base,self.first_imageno+i))
+        else:
+            for i in range(self.th.size):
+                self.filenames.append("%s/%s/%s_%05.cbf" % (path_to_folder,\
+                    self.filename_base,self.filename_base,self.first_imageno+i))
+            
+    def get_raw_PE_img(self,img):
+        return PE_Image(self.filenames[img],self.dark)
+        
+    # returns single default image!
+    def get_raw_img(self,img):
+        return PE_Image(self.filenames[img],self.dark)
+    
+    def get_PE_img(self,img):
+        imgdata = PE_Image(self.filenames[img],self.dark)
+        imgdata.counters['Time'] = self.time[img]
+        imgdata.counters['TrigTime'] = self.exposure_time[img]
+        imgdata.counters['th'] = self.th[img]
+        imgdata.counters['om'] = self.omega[img]
+        if self.current is not None:
+            imgdata.counters['srcur'] = self.current[img]
+        return imgdata
+    
+    def __getitem__(self,key):
+        return self.get_PE_img(key)
+    
+    def __len__(self):
+        return self.nopoints
+        
+    

orgui/backend/beamline/__init__.py

@@ -0,0 +1,36 @@
+# -*- coding: utf-8 -*-
+# /*##########################################################################
+#
+# Copyright (c) 2020-2024 Timo Fuchs
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+__author__ = "Timo Fuchs"
+__copyright__ = "Copyright 2020-2024 Timo Fuchs"
+__license__ = "MIT License"
+__version__ = "1.0.0"
+__maintainer__ = "Timo Fuchs"
+__email__ = "fuchs@physik.uni-kiel.de"
+
+"""Module descripiton
+
+"""
+
+__all__ = ['id31_tools', 'P212_tools']