Supporting Python 3.

A lot of new functionalities.
Production code 12-2023.

Author: MartinSavko

H5ToCBF.py

@@ -136,21 +136,21 @@ def get_header_information(master_file):
     h['oscillation_axis_values'] = master_file["/entry/sample/goniometer/%s" % oscillation_axis.lower()][()]
     image_path = os.path.dirname(os.path.abspath(master_file.filename))
     h['image_path'] = image_path
-    filename_template = master_file.filename.replace('_master.h5', '_#####.cbf')
+    filename_template = master_file.filename.replace('_master.h5', '_######.cbf')
     h['filename_template'] = filename_template
     h['image_numbers'] = get_image_numbers(master_file)
     return h
 
 def get_image_numbers(master_file):
-    data_items = master_file['/entry/data'].items()
+    data_items = list(master_file['/entry/data'].items())
     data_items.sort(key=lambda x: x[0])
     image_numbers=[]
     for key, value in data_items:
         log.debug('key, value: %s, %s' % (key, value))
         try:
             low = value.attrs.get('image_nr_low')
             high = value.attrs.get('image_nr_high')
-            image_numbers += range(low, high+1, 1)
+            image_numbers += list(range(low, high+1, 1))
         except:
             log.exception(traceback.format_exc())
     return image_numbers
@@ -183,10 +183,7 @@ def get_wedges(start, nimages, n_cpu):
     return wedges
 
 def get_nimages(master_file, first, last):
-    #nimages = master_file["/entry/instrument/detector/detectorSpecific/nimages"][()]
-    #ntrigger = master_file["/entry/instrument/detector/detectorSpecific/ntrigger"][()]
-    #nimages *= ntrigger
-    nimages = sum([d.shape[0] for d in master_file['/entry/data'].values() if d is not None])
+    nimages = sum([d.shape[0] for d in list(master_file['/entry/data'][()]) if d is not None])
     if first!=0 and last!=-1 and last>first:
         nimages = last - first
     elif first > 0:
@@ -235,7 +232,7 @@ def extract_cbfs(master_file, master_file_absolute_path, destination_directory,
 def save_image(header_dictionary, master_file_absolute_path, destination_directory, n, compress=None):
     filename_template = header_dictionary['filename_template']
     image_number = header_dictionary['image_numbers'][n] # n+1
-    filename = os.path.basename(filename_template.replace('#####', str(image_number).zfill(5)))
+    filename = os.path.basename(filename_template.replace('######', str(image_number).zfill(6)))
     header_dictionary['filename'] = 'data_%s'  % (filename.replace('.cbf',''))
     omegas = header_dictionary['omegas']
     phis = header_dictionary['phis']
@@ -266,12 +263,12 @@ def save_image(header_dictionary, master_file_absolute_path, destination_directo
 
 
     header = header_template.format(**header_dictionary)
-    header_filename = 'header_%s' % (str(image_number).zfill(5))
+    header_filename = 'header_%s' % (str(image_number).zfill(6))
     f = open(header_filename, 'w')
     f.write(header)
     f.close()
 
-    raw_cbf_filename = '%s.cbf' % str(image_number).zfill(5)
+    raw_cbf_filename = '%s.cbf' % str(image_number).zfill(6)
     H5ToXds_line = 'H5ToXds %s %s %s' % (master_file_absolute_path, image_number, raw_cbf_filename)
     os.system(H5ToXds_line)
     log.debug(H5ToXds_line)
@@ -315,8 +312,8 @@ def get_dataset_filenames(master_file_absolute_path):
     parser.add_option('-O', '--overwrite', action='store_true', help='Overwrite existing files.')
 
     options, args = parser.parse_args()
-    print 'options'
-    print options
+    print('options')
+    print(options)
     if options.n_cpu <= 0:
        options.n_cpu = get_n_cpu()
 
@@ -325,7 +322,7 @@ def get_dataset_filenames(master_file_absolute_path):
     source_directory = os.path.dirname(master_file_absolute_path)
 
     dataset_filenames = get_dataset_filenames(master_file_absolute_path)
-    print 'dataset_filenames', dataset_filenames
+    print('dataset_filenames', dataset_filenames)
 
     for f in dataset_filenames:
         shutil.copy2(f, options.treatment_directory)
@@ -358,11 +355,11 @@ def get_dataset_filenames(master_file_absolute_path):
 
     cbf_files = glob.glob(filename_template)
     if nimages == len(cbf_files) and options.overwrite != True:
-        print 'It seems conversion of %s to cbf has already been done. Please use option --overwrite if you wish to regenerate the files. Exiting ...'
+        print('It seems conversion of %s to cbf has already been done. Please use option --overwrite if you wish to regenerate the files. Exiting ...')
         sys.exit()
 
-    print 'Starting h5 to cbf conversion. The conversion time per image should be below 0.1 second. If it is more, there may be something wrong with the system.'
-    print '%d images to extract. Using %d threads. Processing in %d wedges of %d images.\n' % (nimages, options.n_cpu, len(wedges), len(wedges[0]))
+    print('Starting h5 to cbf conversion. The conversion time per image should be below 0.1 second. If it is more, there may be something wrong with the system.')
+    print('%d images to extract. Using %d threads. Processing in %d wedges of %d images.\n' % (nimages, options.n_cpu, len(wedges), len(wedges[0])))
 
     extract_cbfs(master_file, master_file_absolute_path.replace(source_directory, options.treatment_directory), destination_directory, options.first, options.last, options.n_cpu, compress)
 

XDS_from_H5.py

@@ -7,10 +7,10 @@
 try:
    import albula as dec
 except ImportError:
-   print "\nThe DECTRIS ALBULA API could not be loaded."
-   print "If you did not install ALBULA with \"--python=</path/to/python_interpreter>\","
-   print "please modify the \'sys.path.insert\' line in the script to point"
-   print "to the DECTRIS ALBULA API and uncomment the line."
+   print("\nThe DECTRIS ALBULA API could not be loaded.")
+   print("If you did not install ALBULA with \"--python=</path/to/python_interpreter>\",")
+   print("please modify the \'sys.path.insert\' line in the script to point")
+   print("to the DECTRIS ALBULA API and uncomment the line.")
    raise SystemExit
 
 import os.path
@@ -447,15 +447,15 @@ def request_parameter(parameter):
     elif (parameter == nimages):
         return raw_input("Please enter the number of images.\n")
     elif (parameter == description):
-        print "Please enter the description of the detector, e.g."
+        print("Please enter the description of the detector, e.g.")
         return raw_input("Dectris Eiger 4M\n")
     elif (parameter == countrate_correction_count_cutoff):
         return raw_input("Please enter the maximum trusted pixel value.\n")
     elif (parameter == resolution_cutoff):
         #return raw_input("Please enter a resolution limit for processing.\n")
         return 0
     else:
-        print "Unknown software version.  Please check."
+        print("Unknown software version.  Please check.")
         return 0
 
 def calculate_gaps(det_size, mod_size, gap_size):
@@ -503,8 +503,8 @@ def get_params(hdf5_file):
     neXus_root = neXus_tree.root()
     neXus_string_tree = iterate_children(neXus_root)
     if (len(sys.argv) == 2):
-        print "Extracting metadata from " + hdf5_file
-        print "Please modify XDS.INP if these numbers are incorrect.\n"
+        print("Extracting metadata from " + hdf5_file)
+        print("Please modify XDS.INP if these numbers are incorrect.\n")
     for i in parameters:
         if (neXus_string_tree.has_key(i)):
             extracted[i] = str(neXus_string_tree[i])
@@ -530,40 +530,40 @@ def calculate_size(n_modules, mod_size, gap_size):
     if len(sys.argv) == 2:
         # Make sure that XDS.INP does not already exist
         if os.path.isfile ("XDS.INP"):
-            print "\nERROR: XDS.INP exists already.  Please rename and rerun script."
+            print("\nERROR: XDS.INP exists already.  Please rename and rerun script.")
         else:
             # test whether argument 1 is HDF5 file.
             # attach ".h5" if necessary
             clean_file = isFile(sys.argv[1])
             if (clean_file):
-                print warning()
+                print(warning())
                 full_parameters = get_params(clean_file)
                 for i, v in full_parameters.iteritems():
                     if (v in zero_values):
-                        print i + " = " + str(v) + "   <== WARNING:  Should this really be 0?"
+                        print(i + " = " + str(v) + "   <== WARNING:  Should this really be 0?")
                         full_parameters[i] = request_parameter(i)
-                        print i + " = " + str(full_parameters[i])
+                        print(i + " = " + str(full_parameters[i]))
                     elif (v == "NaN") or (v == ""):
-                        print i + " = " + v + "   <== ERROR:  undefined value."
+                        print(i + " = " + v + "   <== ERROR:  undefined value.")
                         full_parameters[i] = request_parameter(i)
-                        print i + " = " + str(full_parameters[i])
+                        print(i + " = " + str(full_parameters[i]))
                     else:
-                        print i + " = " + str(v)
+                        print(i + " = " + str(v))
                 para_version = str(full_parameters[software_version])
                 if version_check(para_version):
                     param_lines = create_XDS_INP(full_parameters, clean_file)
                     open("XDS.INP", 'w').writelines(param_lines)
-                    print "\nFile XDS.INP was created successfully."
+                    print("\nFile XDS.INP was created successfully.")
                     if (int(full_parameters["/entry/instrument/detector/detectorSpecific/nimages"]) == 1):
-                        print "However, there's not much you can do with one image.\n"
+                        print("However, there's not much you can do with one image.\n")
                     else:
-                        print "Please verify its contents before processing data.\n"
+                        print("Please verify its contents before processing data.\n")
                 else:
-                    print "\nThe HDF5 file was created with version %s of the detector firmware" % (para_version)
-                    print "This script supports versions 1.5 and up."
-                    print "Please extract metadata with hdfview or h5dump.\n"
+                    print("\nThe HDF5 file was created with version %s of the detector firmware" % (para_version))
+                    print("This script supports versions 1.5 and up.")
+                    print("Please extract metadata with hdfview or h5dump.\n")
             else:
-                print help()
+                print(help())
     elif (len(sys.argv) == 3):
         # This assumes the second argument is the rotation range
         # The script will run non-interactively
@@ -574,6 +574,6 @@ def calculate_size(n_modules, mod_size, gap_size):
         param_lines = create_XDS_INP(full_parameters, sys.argv[1])
         open("XDS.INP", 'w').writelines(param_lines)
     else:
-        print help()
+        print(help())
         exit(-1)
 

adxv_follow

@@ -0,0 +1,30 @@
+#!/bin/bash 
+# Pierre Legrand ([email protected])
+
+# kill previous adxv with socket option
+function pid_adxv_follow () {
+    echo $(ps -ef | grep adxv | grep socket | tail -1 | awk '{print $2 }')
+}
+
+pid=$(pid_adxv_follow)
+while [ ! -z $pid ]; do
+   kill -9 $pid
+   pid=$(pid_adxv_follow)
+done
+
+export ADXV_SHOW_PIXELS="120000" 
+# export ADXV_PATTERN="*.h5"
+export ADXV_PATTERN="*.*"
+export OMP_NUM_THREADS=10
+export MARHOME=${prog_dir}
+#exec_file=/usr/local/bin/adxv.x86_64Centos5
+exec_file=/data/bioxsoft/bin/adxv
+
+if [ $# -gt 0 ]
+  then
+    echo "Loading adxv in directory $1"
+    cd $1
+fi
+
+exec $exec_file -slabs 10 -fix_contrast -small_spots -verbose -socket -parallel -rings -socket_no_list_files -no_default_win_pos -no_adxv_beam_center -dectris_kludge -dectris_kludge2 "$@"
+

adxv_follow_embl

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+LOGFILE=$HOME/adxv.log
+
+export OMP_NUM_THREADS=10
+export ADXV_PATTERN="*.*"
+export ADXV_SHOW_PIXELS="120000"
+adxv -parallel -rings -socket_no_list_files -slabs 10 -socket -no_default_win_pos -no_adxv_beam_center -dectris_kludge -dectris_kludge2 | tee -a %LOGFILE | grep --line-buffered -e "Loading" -e "Unknown file type:" -e "read error" -e "No such file " -e "Warning: " -e "is not and file" -e "is not a file" | ncat --broker -l -k 7100 &
+
+