Merge branch 'alessandro_develop'

.gitlab-ci.yml

-test3:
-  stage: test
-  only:
-    - scisoft12
-  tags:
-    - scisoft12
-  script:
-    - echo 'current dir is '
-    - pwd
-    - unset PYTHONPATH
-    - export PATH=/usr/local/bin:/usr/bin:/bin:/opt/oar/utilities:/sbin:/usr/bin/X11:.::.
-    - unset LDFLAGS
-    - unset CPPFLAGS
-    - unset LD_LIBRARY_PATH
-    - rm -rf ~/software/virtualenv_xrstools_python3/
-    - virtualenv --python=python3 ~/software/virtualenv_xrstools_python3/
-    - source ~/software/virtualenv_xrstools_python3/bin/activate
-    - pip install setuptools --upgrade
-    - pip install pip --upgrade
-    - pip install numpy
-    - pip install -r requirements.txt
-    - ln -s  /usr/lib/python3/dist-packages/PyQt* ~/software//virtualenv_xrstools_python3/lib/python3.4/site-packages/
-    - ln -s  /usr/lib/python3/dist-packages/sip* ~/software//virtualenv_xrstools_python3/lib/python3.4/site-packages/
-    - pip install .
-    - cd nonregressions
-    - /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python non_reg_testing_XRS.py
-    - /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python non_reg_testing_XRS_small.py
-    - /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python non_reg_testing_XRS_raman_extraction.py
-    - deactivate
-    
-  after_script:
-    - pwd
-    
+stages:
+  - test
+#  - deploy
+
+variables:
+  PROJECT_NAME: "xrstools"
+  LOCAL_REPO: "/dev/shm/gitlab_ci/xrstools"
+  VENV_DIR: /dev/shm/gitlab_ci/xrstools/venv
+  USE_CLEAN_VENV: "false"
+  CLEAN_RESULTS: "true"
+
 test:
   stage: test
   only:
-    - scisoft13
+    - nocdi
   tags:
-    - scisoft13
-  script:
-    - echo 'current dir is '
-    - pwd
-    - unset PYTHONPATH
-    - export PATH=/usr/local/bin:/usr/bin:/bin:/opt/oar/utilities:/sbin:/usr/bin/X11:.::.
-    - unset LDFLAGS
-    - unset CPPFLAGS
-    - unset LD_LIBRARY_PATH
-    - rm -rf ~/software/virtualenv_xrstools_python2/
-    - virtualenv --python=python2 ~/software/virtualenv_xrstools_python2/
-    - source ~/software/virtualenv_xrstools_python2/bin/activate
-    - pip install setuptools --upgrade
-    - pip install pip --upgrade
-    - pip install numpy
+    - scisoft10
+  before_script:
+    - unset HTTP_PROXY
+    - unset HTTPS_PROXY
+    - if [ ! -d $LOCAL_REPO ]; then mkdir -p $LOCAL_REPO; fi
+    - if [ -d $VENV_DIR ]; then if [ "$USE_CLEAN_VENV" == "true" ]; then rm -rf $VENV_DIR; fi; fi
+    - python3 -m venv $VENV_DIR
+    - source $VENV_DIR/bin/activate
+    - echo "Running $(python --version) from $(which python) on $(hostname) ($(arch))"
+ 
+    - pip install  --upgrade  pip setuptools wheel
+    - pip install --upgrade numpy silx
+    - pip install PyQt5  
     - pip install -r requirements.txt
-    - ln -s  /usr/lib/python2.7/dist-packages/PyQt* ~/software//virtualenv_xrstools_python2/lib/python2.7/site-packages/
-    - ln -s  /usr/lib/python2.7/dist-packages/sip* ~/software//virtualenv_xrstools_python2/lib/python2.7/site-packages/
     - pip install .
-    - cd nonregressions
-    - /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python non_reg_testing_XRS.py
-    - /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python non_reg_testing_XRS_small.py
-    - /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python non_reg_testing_XRS_raman_extraction.py
-    - deactivate
-    
-  after_script:
-    - pwd
 
-testnslino:
-  stage: test
-  only:
-    - nslino
-  tags:
-    - nslino
   script:
-    - echo 'current dir is '
     - pwd
-    - unset PYTHONPATH
-    - export PATH=/usr/local/bin:/usr/bin:/bin:/opt/oar/utilities:/sbin:/usr/bin/X11:.::.
-    - unset LDFLAGS
-    - unset CPPFLAGS
-    - unset LD_LIBRARY_PATH
-    - rm -rf ~/software/virtualenv_xrstools_python2/
-    - virtualenv --python=python2 ~/software/virtualenv_xrstools_python2/
-    - source ~/software/virtualenv_xrstools_python2/bin/activate
-    - pip install setuptools --upgrade
-    - pip install pip --upgrade
-    - pip install numpy
-    - pip install -r requirements.txt
-    - ln -s  /usr/lib/python2.7/dist-packages/PyQt* ~/software//virtualenv_xrstools_python2/lib/python2.7/site-packages/
-    - ln -s  /usr/lib/python2.7/dist-packages/sip* ~/software//virtualenv_xrstools_python2/lib/python2.7/site-packages/
-    - pip install .
-    - cd nonregressions
-    - /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python non_reg_testing_XRS.py
-    - /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python non_reg_testing_XRS_small.py
-    - /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python non_reg_testing_XRS_raman_extraction.py
+    - cd nonregressions/xes
+    - /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python xes_analysis.py >| output
+    - cd ../xrs_raman
+    - /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python non_reg_testing_XRS.py >| output1
+    - /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python non_reg_testing_XRS_small.py >| output2
+    - /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python non_reg_testing_XRS_raman_extraction.py >| output3
+    - cd ../volumes/test1
+    - /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python test.py >| output
     - deactivate
-    
   after_script:
     - pwd
-
-
-
-test3nslino:
-  stage: test
-  only:
-    - nslino3
-  tags:
-    - nslino
-  script:
-    - echo 'current dir is '
-    - pwd
-    - unset PYTHONPATH
-    - export PATH=/usr/local/bin:/usr/bin:/bin:/opt/oar/utilities:/sbin:/usr/bin/X11:.::.
-    - unset LDFLAGS
-    - unset CPPFLAGS
-    - unset LD_LIBRARY_PATH
-    - rm -rf ~/software/virtualenv_xrstools_python3/
-    - virtualenv --python=python3 ~/software/virtualenv_xrstools_python3/
-    - source ~/software/virtualenv_xrstools_python3/bin/activate
-    - pip install setuptools --upgrade
-    - pip install pip --upgrade
-    - pip install numpy
-    - pip install -r requirements.txt
-    - pip install PyQt5
-    - pip install .
-    - cd nonregressions
-    - /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python non_reg_testing_XRS.py
-    - /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python non_reg_testing_XRS_small.py
-    - /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python non_reg_testing_XRS_raman_extraction.py
-    - deactivate
     
-  after_script:
-    - pwd
+ 
\ No newline at end of file

.gitmodules

+[submodule "HighFive"]
+	path = fitcc/HighFive
+	url = https://github.com/BlueBrain/HighFive.git

XRStools/XES_spectra_extraction.py

+import os
+import json
+import h5py
+import numpy as np
+
+
+
+def runit( s , work_dir, filename ) :
+    open(  os.path.join(work_dir, filename) ,"w" ).write(s)
+    os.system( "cd %s; XRS_swissknife %s ; cd .." % (work_dir, filename)  )
+
+
+def prepare(
+        work_dir="preparation_run4_16",
+        data = "/data/id20/inhouse/data/run4_16/run6_ihr/rixs" ,
+        scan_for_roi= 66            ,
+
+        do_roi = True,
+        do_roi_sample = True, 
+
+        reference_scan = 66 ,              # the scan used for the reference
+        monitorcolumn = "izero",
+        do_recentering=False,
+        scan_for_sample_roi =  268  ,           # Not necessary is recentering is not needed. If not given the rois file is assumed (when needed if needed) to be already there
+        beta_response = 0
+) :
+    if not os.path.exists(work_dir):
+        os.makedirs(work_dir)
+    assert (os.path.exists( work_dir) and os.path.isdir( work_dir)  ), "Cannot get work directory %s "%work_dir    
+    assert (os.access(work_dir, os.W_OK | os.X_OK)), " directory %s is not writable"%work_dir 
+            
+    preparation_parameters = {
+        "work_dir" : work_dir,
+        "data" : data,
+        "scan_for_roi" : scan_for_roi, 
+        "reference_scan" : reference_scan,
+        "monitorcolumn" : monitorcolumn,
+        "do_recentering" : do_recentering,
+        "scan_for_sample_roi" : scan_for_sample_roi   
+    }
+
+    json.dump(preparation_parameters, open(os.path.join(work_dir, "preparation_parameters.json"),"w")  )
+
+
+    if do_roi:
+        s="""
+        create_rois:
+          expdata : "{data_file}" 
+          scans : [{scan_for_roi}] 
+          roiaddress : "roi.h5:/ROI_AS_SELECTED" 
+        """.format( data_file = data,  scan_for_roi = scan_for_roi )
+
+        runit( s , work_dir, "01_create_roi.yaml" )
+        
+
+    if do_recentering and do_roi_sample:
+        s="""
+        create_rois:
+          expdata : "{data_file}" 
+          scans : [{scan_for_roi} ] 
+          roiaddress : roi_sample.h5:/ROI_AS_SELECTED 
+        """.format( data_file = data,  scan_for_roi = scan_for_sample_roi )
+
+        runit( s , work_dir, "02_create_roi_sample.yaml" ) 
+
+        
+    s="""
+    loadscan_2Dimages :
+      expdata :  "{data_file}" 
+      roiaddress : roi.h5:/ROI_AS_SELECTED 
+      scan_interval : [{reference_scan},{reference_scan_P1}] 
+      signaladdress : calibration_scan 
+      sumto1D  : 0
+      energycolumn : 'Anal Energy'
+      monitorcolumn : {monitorcolumn}
+      save_also_roi : 1
+    """.format( data_file = data,  reference_scan = reference_scan , reference_scan_P1 = reference_scan +1 , monitorcolumn = monitorcolumn )
+    runit( s , work_dir, "03_load_scan_reference.yaml" ) 
+
+
+
+
+    if do_recentering : 
+        s="""
+        loadscan_2Dimages :
+          expdata :  "{data_file}" 
+          roiaddress : roi_sample.h5:/ROI_AS_SELECTED 
+          scan_interval : [{scan_for_roi},{scan_for_roi_P1}] 
+          signaladdress : uncentered_sample_scan 
+          sumto1D  : 0
+          energycolumn : 'Anal Energy'
+          monitorcolumn : {monitorcolumn}
+          save_also_roi : 1
+        """.format( data_file = data,  scan_for_roi = scan_for_sample_roi , scan_for_roi_P1 = scan_for_sample_roi +1 , monitorcolumn = monitorcolumn )
+        runit( s , work_dir, "04_load_scan_sample.yaml" ) 
+
+
+        s="""
+        calculate_recenterings :
+           bariA : roi_sample.h5:/ROI_AS_SELECTED/uncentered_sample_scan/scans/Scan%03d/ 
+           bariB : roi.h5:/ROI_AS_SELECTED/calibration_scan/scans/Scan%03d/ 
+           target : recentering.h5:/recentering
+        """%( scan_for_sample_roi,  reference_scan )
+        runit( s , work_dir, "05_setup_recentering.yaml" ) 
+        
+
+        s="""
+        loadscan_2Dimages :
+          expdata : {data_file}
+          roiaddress : roi.h5:/ROI_AS_SELECTED 
+          scan_interval : [{scan_for_roi},{scan_for_roi_P1}] 
+          monitorcolumn : {monitorcolumn}
+          recenterings  : recentering.h5:/recentering
+          recenterings_confirmed : recentering.h5:/confirmed_shift 
+          signaladdress : Centered_sample_scans 
+
+          sumto1D  : 0
+          energycolumn : 'Anal Energy'
+        """.format( data_file = data,  scan_for_roi = scan_for_sample_roi , scan_for_roi_P1 = scan_for_sample_roi +1 , monitorcolumn = monitorcolumn )
+        runit( s , work_dir, "06_calculate_recentering.yaml" ) 
+
+        s="""
+        superR_fit_responses:
+           foil_scan_address : roi.h5:/ROI_AS_SELECTED/calibration_scan/scans/Scan%03d
+           nref : 2 
+           niter_optical : 50 
+           beta_optical : %e
+           niter_global : 2 
+           pixel_dim  : 1 
+           niter_pixel : 0 
+           beta_pixel :  0 
+           do_refine_trajectory  : 1 
+           simmetrizza : 1
+           filter_rois : 0
+           target_file : fitted_response.h5:/ScanFittedResponse_%03d
+           fit_lines   : 1 
+        """%( reference_scan, beta_response, reference_scan ) 
+        runit( s , work_dir, "07_fit.yaml" ) 
+
+
+        s="""
+        superR_recreate_rois :
+           responsefilename : fitted_response.h5:/ScanFittedResponse_%03d
+           nex : 0 
+           old_scan_address : roi.h5:/ROI_AS_SELECTED/calibration_scan/scans/Scan%03d
+           filter_rois : 0
+           recenterings_refined : recentering.h5:/confirmed_shift
+           target_filename : newscan.h5:/ROI_AS_SELECTED/calibration_scan/scans/ScanReSynth_%03d
+        """%( reference_scan,  reference_scan,  reference_scan ) 
+        runit( s , work_dir, "08_resynth.yaml" ) 
+
+
+
+def extract(
+        work_dir="preparation_run4_16",
+        scan_interval = [130, 132] ,
+        target_file = "SPECTRA.h5",
+        temporary_file = "temporary.h5",
+        niter = 0,
+        niterLip = 20,
+        beta = 0,    
+        
+) :
+    assert (os.path.exists( work_dir) and os.path.isdir( work_dir)  ), "Cannot get work directory %s "%work_dir    
+    assert (os.access(work_dir, os.W_OK | os.X_OK)), " directory %s is not writable"%work_dir 
+
+    preparation_parameters = json.load( open(os.path.join(work_dir, "preparation_parameters.json"),"r")  )
+
+    data = preparation_parameters["data"]
+    reference_scan = preparation_parameters["reference_scan"]
+    monitorcolumn = preparation_parameters["monitorcolumn"]
+    scan_for_roi = preparation_parameters["scan_for_roi"]
+
+    start =  scan_interval[0]
+    end   = scan_interval[1]
+    
+    s="""
+    loadscan_2Dimages :
+      expdata : {data_file}
+      roiaddress : newscan.h5:/ROI_AS_SELECTED/calibration_scan/scans/ScanReSynth_{reference_scan:03d}
+      scan_interval : [{start}, {end}]
+      signaladdress : ../{temporary_file}:/data_{start}_{end} 
+      sumto1D  : 0
+      energycolumn : 'Anal Energy'
+      monitorcolumn : {monitorcolumn}
+    """.format(data_file = data,  reference_scan = reference_scan ,  monitorcolumn = monitorcolumn,
+               start = start, end = end, temporary_file=temporary_file)
+    runit( s , work_dir, "31_harvest.yaml" ) 
+    
+
+    s="""
+    extract_spectra :
+     reference_address : newscan.h5:/ROI_AS_SELECTED/calibration_scan/scans/ScanReSynth_{reference_scan:03d}
+     sample_address : ../{temporary_file}:/data_{start}_{end} 
+     roiaddress :     newscan.h5:/ROI_AS_SELECTED/calibration_scan/scans/ScanReSynth_{reference_scan:03d}
+     reference_scan : {reference_scan}
+     scan_interval : [{start}, {end}]
+     zmargin : 0
+     target : ../{result_file}:/fromscans_{start}_{end}
+     # final_plot : PLOT
+     DE : 0.0
+     niterLip : {niterLip}
+     niter : {niter}
+     beta :   {beta}
+    """.format(reference_scan=reference_scan, start = start, end = end , niterLip = niterLip, niter = niter, beta = beta, result_file = target_file, temporary_file=temporary_file)
+    runit( s , work_dir, "32_extract_spectra.yaml" ) 

XRStools/fit_spectra.py

@@ -36,7 +36,7 @@ def Fista(solution   ,  problem,   niter, niterLip):
     x_old  = solution
 
     errList=[]
-    for i in range(1000):
+    for i in range(niter):
         grad, err = problem.calculate_grad(y)
         print( "err " , err)
         errList.append(err)

XRStools/myMaskImageWidget.py

@@ -46,8 +46,8 @@ class MaskImageWidget(sole_MaskImageWidget.MaskImageWidget):
                         self.plotImage(update = False)
                         self._emitMaskChangedSignal()
                     return
-        # super(MaskImageWidget, self)._graphSignal(ddict, ownsignal) 
-        sole_MaskImageWidget.MaskImageWidget._graphSignal(self, ddict, ownsignal)
+        super(MaskImageWidget, self)._graphSignal(ddict, ownsignal) 
+        # sole_MaskImageWidget.MaskImageWidget._graphSignal(self, ddict, ownsignal)
 
 
     def dragEnterEvent(self,event):

XRStools/ramanWidget/MainWindow.py

@@ -685,7 +685,7 @@ class plotContainer(QtGui.QWidget) :
 
         if len(regionNorm):
             norm = np.trapz(data[regionNorm,1],data[regionNorm,0])
-            print(" NOOOOOOOOOOOOOOOOOOOOOOOOOOOORM ", norm)
+            print(" NORM ", norm)
             data[:,1] /= norm
             data[:,2] /= norm
         np.savetxt(prefix+"_"+self.name+".txt",data)

XRStools/reponse_percussionelle.py

@@ -6,6 +6,7 @@ import math
 import scipy
 import scipy.stats
 import scipy.ndimage.filters as filt
+from scipy.ndimage import gaussian_filter 
 import sys
 import pickle
 import os
@@ -377,7 +378,7 @@ def    Fista( data , solution   ,   s2d, d2s, solution_shape , parallel = 0 , ni
 
     if myrank==0:
         print( indent+"CALCULATING LIPSCHITZ FACTOR ")
-    for i in range(100):
+    for i in range(10):
         calculate_grad(grad2,None ,grad , s2d, d2s, solution_shape , parallel = parallel , beta=beta)
         Lip = math.sqrt( np.linalg.norm(grad2/100000)   )*100000
         grad[:]  = grad2/ Lip
@@ -725,8 +726,11 @@ def get_spots_list(  filename  , groupname , filter_rois =1 ):
 
     xscales = {}
     enescan = None
+
+    tmp_list = list(filterRoiList(list(h5[groupname].keys())))
+    tmp_list = sorted(tmp_list, key = int )
     
-    for sn in filterRoiList(list(h5[groupname].keys())):
+    for sn in tmp_list:
         
         print( groupname+"/"+sn+"/matrix")
         m  = h5[groupname+"/"+sn+"/matrix"][:]
@@ -740,7 +744,7 @@ def get_spots_list(  filename  , groupname , filter_rois =1 ):
 
         
         if groupname+"/motorDict/energy" in h5:
-            enescan = h5[groupname+"/motorDict/energy"].value
+            enescan = h5[groupname+"/motorDict/energy"][()]
 
         
         if m.shape!=(0,):
@@ -876,7 +880,7 @@ def DOFIT(filename=None, groupname=None, nref=5, niter_optical=500, beta_optical
 
     O_spots_list, nomi_rois, stats, origini_foil, rois, xscales, energy = get_spots_list( filename,  groupname,  filter_rois= filter_rois )
     stats = np.array(stats)
-    
+
     if do_refine_trajectory ==2:
 
         h5f = h5py.File(trajectory_reference_scansequence_filename,"r")
@@ -1010,7 +1014,6 @@ def DOFIT(filename=None, groupname=None, nref=5, niter_optical=500, beta_optical
 
 
         print(  nomi_rois)
-        print(  O_spots_list)
         for iterm, (O_spots, name, ROI )  in enumerate(zip(O_spots_list, nomi_rois, rois)):
             if (iterm)%nprocs == myrank:
                 # print " MYRANK %d fa "%myrank, iterm
@@ -1196,10 +1199,10 @@ def reload_trajectories(trajectory_file, nomi_rois) : ### , trajectory_file_grou
     for iterm,  name  in enumerate( nomi_rois[:]):
         h5group = h5[name]
         trajectory = Trajectory()
-        trajectory.X.intercept  = h5group["Xintercept"].value
-        trajectory.X.slope      = h5group["Xslope"].value
-        trajectory.Y.intercept  = h5group["Yintercept"].value
-        trajectory.Y.slope      = h5group["Yslope"].value
+        trajectory.X.intercept  = h5group["Xintercept"][()]
+        trajectory.X.slope      = h5group["Xslope"][()]
+        trajectory.Y.intercept  = h5group["Yintercept"][()]
+        trajectory.Y.slope      = h5group["Yslope"][()]
         # trajectory.N            = O_spots.shape[0]
         trajectory_list.append( trajectory ) 
     return trajectory_list
@@ -1209,17 +1212,22 @@ def reload_trajectories(trajectory_file, nomi_rois) : ### , trajectory_file_grou
 
 
 def DOROIS(filename = "../nonregressions/demo_imaging.hdf5" , groupname = "ROI_B/foil_scanXX/scans/Scan273/",
+           roi_filename = None, 
            roisgroupname = "ROI_B/",
            target_filename="newscan.h5", 
            roisgroupname_target = "ROI_B_FIT8/",
            newscanstarget    = "scanXX/scans/Scan273",
            responsefilename =  "responses.h5",
+           resynth_z_square = None,
            responsepath =  "fit",
            nex = 3,
            filter_rois=1,
            recenterings= None,
            filterMask = None):
-    
+
+
+    if roi_filename is None:
+        roi_filename = filename
     O_spots_list, nomi_rois, stats , origini, rois, xscales, energy= get_spots_list( filename,  groupname ,  filter_rois= filter_rois  )
 
     trajectory_list = []
@@ -1231,7 +1239,6 @@ def DOROIS(filename = "../nonregressions/demo_imaging.hdf5" , groupname = "ROI_B
     
     for iterm,  (O_spots, name)  in enumerate(zip(O_spots_list[:], nomi_rois[:])):
 
-
         if (iterm)%nprocs == myrank:
 
             if myrank ==0 :
@@ -1239,13 +1246,16 @@ def DOROIS(filename = "../nonregressions/demo_imaging.hdf5" , groupname = "ROI_B
 
             h5group = h5[name]
             print( name, "data")
-            solution =  h5group["data"][:]
+            solution =  h5group["data"][()]
             trajectory = Trajectory()
-            trajectory.X.intercept  = h5group["Xintercept"].value
-            trajectory.X.slope      = h5group["Xslope"].value
-            trajectory.Y.intercept  = h5group["Yintercept"].value
-            trajectory.Y.slope      = h5group["Yslope"].value
-            nref                    = h5group["nref"].value
+            trajectory.X.intercept  = h5group["Xintercept"][()]
+            trajectory.X.slope      = h5group["Xslope"][()]
+            trajectory.Y.intercept  = h5group["Yintercept"][()]
+            trajectory.Y.slope      = h5group["Yslope"][()]
+            nref                    = h5group["nref"][()]
+            if resynth_z_square is not None:
+                solution = gaussian_filter( solution, [  nref*resynth_z_square  , 0 ])
+            
             trajectory.N            = O_spots.shape[0]
 
             if recenterings is not None:
@@ -1261,7 +1271,7 @@ def DOROIS(filename = "../nonregressions/demo_imaging.hdf5" , groupname = "ROI_B
             trajectory.Y.intercept += -recy
 
             if "line" in h5group:
-                trajectory.line = h5group["line"].value
+                trajectory.line = h5group["line"][()]
                 lh,lslope =trajectory.line
                 lh = lh-recy + recx*lslope
                 trajectory.line = np.array([lh,lslope])
@@ -1304,13 +1314,15 @@ def DOROIS(filename = "../nonregressions/demo_imaging.hdf5" , groupname = "ROI_B
             # print( filename)
             # print( roisgroupname+ "/rois_definition/image")
             
-            h5f = h5py.File(filename,"r")
+            h5f = h5py.File( roi_filename,"r")
             
             # imagealldect =  h5f [roisgroupname+ "/rois_definition/image"][:]
+            print( roi_filename)
+            print( roisgroupname+ "/image" )
             imagealldect =  h5f [roisgroupname+ "/image"][:]
-
+            
             # h5 = h5f [roisgroupname+  ("/rois_definition/rois_dict/ROI%02d"%int(name)) ]
-            h5 = h5f [roisgroupname+  ("/ROI%02d"%int(name)) ]
+            h5 = h5f [roisgroupname+  ("/rois_dict/ROI%02d"%int(name)) ]
             mask   = h5["mask"  ][:]
             origin = h5["origin"][:]
             h5f.close()
@@ -1427,7 +1439,17 @@ def DOROIS(filename = "../nonregressions/demo_imaging.hdf5" , groupname = "ROI_B
             
             h5.require_group( str(name)  )
             h5 = h5 [str(name)   ]
+
+            
+            for i in range(len(newspots)):
+                spot_sum = newspots[i].sum()
+                if spot_sum:
+                    newspots[i] = newspots[i]/spot_sum
+
+                
             h5["matrix"] = newspots
+
+            
             h5["Xintercept"] =trajectory.X.intercept
             h5["Yintercept"] =trajectory.Y.intercept
             h5["Xslope"] =trajectory.X.slope

XRStools/roiSelectionWidget.py

@@ -267,6 +267,7 @@ class mainwindow(Qt.QMainWindow):
         self.close()
     def confirm_and_Exit(self):
         self.isOK=1
+        self.roiobj_returned = self.getRoiObj()      
         self.close()
 
     def remoteMaskload(self):
@@ -1272,9 +1273,16 @@ def launch4MatPlotLib(layout=None, im4roi=None, manageQApp = True):
     
     if manageQApp:
         app.exec_()
+        if w4r.isOK:
+            return_obj = w4r.getRoiObj()
+
+        else:
+            return_obj = None
         if dostop:
             app.quit()
+        return     return_obj
 
+        
             
     return w4r
 

XRStools/superr.py

@@ -57,7 +57,7 @@ def my_denoise_tv_chambolle_positive(image, weight=0.1,  n_iter_max=200):
         
 
 def _denoise_tv_chambolle_nd(image, weight=0.1, eps=2.e-4, n_iter_max=200,
-                             positivity=False):
+                             positivity=False, cdim = None):
     """Perform total-variation denoising on n-dimensional images.