Normalise line endings

nexusformat · Dec 10, 2015 · 662de93 · 662de93
1 parent 227079d
commit 662de93
Show file tree

Hide file tree

Showing 37 changed files with 17,986 additions and 17,986 deletions.
diff --git a/cmake_include/FindJNI.cmake b/cmake_include/FindJNI.cmake
diff --git a/cmake_include/FindJava.cmake b/cmake_include/FindJava.cmake
diff --git a/cmake_include/Utilities.cmake b/cmake_include/Utilities.cmake
diff --git a/contrib/applications/NXextract/example/template_1.nxe b/contrib/applications/NXextract/example/template_1.nxe
@@ -1,119 +1,119 @@
-#==============================================================================
-# File: 
-#	Multiframes_to_EDF.nxe
-#
-# @desc	Produce a EDF (ESRF Data Format) file for each image captured in 'multiframe' CCD camera mode
-#
-# @param dir directory 'Target directory for extracted data' $(_data_extraction_folder_)
-# @param header_length number 'EDF file header length' 4096
-#
-# Usage:
-#	nxextractor -t Multiframes_to_EDF.nxe -D dir=<destination directory> [-m <mode>] [-w uid:gid] <NeXus source file>
-#
-# $Author: poirier $
-#
-# $Revision: 1.7 $
-#==============================================================================
-
-# output to console
->
-"%s\n" $(_FILE_NAME_)
-
-# loop other all entries
-# variable $(entry) will contain current entry path (ex: '/entry1')
-# variable $(entry_name) will contain curren tentry name (ex: 'entry1')
-@( entry = [nxs:/<NXentry>/]
-
-	# loop other range [0, n[
-	@( i = 0, nxs:$(entry)<NXentry>/<NXinstrument>/<NXdetector>/Frames/data
-
-		# define a new variable
-		% image_grp = $(entry)<NXentry>/image#$(i)<NXdata>
-		
-		# define image name for edf file name using a data bloc named 'image_name'
-		( image_name
-			"im_%02d" $(i)
-		)
-		
-		# define variable
-		% image_full_name = $(entry_name)_$(image_name)
-
-		# Test data dimensions
-		?( nxs:$(image_grp)/<SDS-signal>._rank_ = 2
-
-			# Define data bloc for image data
-			( binarydata
-				# output into this bloc as 2 bytes unsigned integers
-				'ui2' nxs:$(image_grp)/<SDS-signal> 
-			)
-			
-			# Define data bloc in memory for EDF header base content
-			( edf_header
-			
-				"EDF_DataBlockID = 1.Image.Psd ;\n"
-				"EDF_BinarySize = %s ;\n" $(binarydata_size)
-				"EDF_HeaderSize = %s ;\n" $(header_length)
-				"ByteOrder = LowByteFirst ;\n"
-				"DataType = UnsignedShort ;\n"
-				"Dim_1 = %d ;\n" nxs:$(image_grp)/data._size_(1)
-				"Dim_2 = %d ;\n" nxs:$(image_grp)/data._size_(2)
-				"Title = %s ;\n" $(image_full_name)
-				"Time =  ;\n"
-				"HeaderID = EH:000001:000000:000000 ;\n"
-				"Compression = None ;\n"
-				"Image = 1 ;\n"
-				"Size = %s ;\n" $(binarydata_size)
-			)
-
-			# Define data bloc for specific metadata
-			( specific_metadata
-				# loop other all NXintensity_monitor groups inside first (and unique) NXinstrument group
-				@( mi_channel = [nxs:$(entry)/<NXinstrument>/<NXintensity_monitor>]
-					"Intensity(%s) = %g ;\n" $(mi_channel_name), nxs:$(mi_channel)/intensity[i]
-					"Gain(%s) = %g ;\n" $(mi_channel_name), nxs:$(mi_channel)/Gain/data
-					"Offset(%s) = %g ;\n" $(mi_channel_name), nxs:$(mi_channel)/offset/data
-				@)
-				
-				"Machine_Current = %? ;\n" nxs:$(entry)/<NXinstrument>/<NXsource>/current
-				"Monochromator_energy = %?%s ;\n" nxs:$(entry)/<NXinstrument>/<NXmonochromator>/energy, nxs:$(entry)/<NXinstrument>/<NXmonochromator>/energy.units
-				"Distance_sample-detector = %?mm ;\n" nxs:$(entry)/<NXinstrument>/<NXdetector>/distance
-				
-				# aviex parameters
-				"_diffrn_detector.detector = %s ;\n" nxs:$(entry)/<NXinstrument>/<NXdetector>/type
-				"Exposure_time  = %?%s ;\n" nxs:$(entry)/<NXinstrument>/<NXdetector>/Exposure/data, nxs:$(entry)/<NXinstrument>/<NXdetector>/Exposure/data.units
-				"Shutter_close_delay  = %?%s ;\n" nxs:$(entry)/<NXinstrument>/<NXdetector>/ShutterCloseDelay/data, nxs:$(entry)/<NXinstrument>/<NXdetector>/ShutterCloseDelay/data.units
-				"Xbin = %? ;\n" nxs:$(entry)/<NXinstrument>/<NXdetector>/Xbin/data
-				"Ybin = %? ;\n" nxs:$(entry)/<NXinstrument>/<NXdetector>/Ybin/data
-				
-				# motors
-				@( motor_data = [nxs:$(entry)/<NXinstrument>/<NXpositioner>]
-					"Position(%s) = %g ;\n" $(motor_data_name), nxs:$(motor_data)/raw_value
-				@)
-			)
-
-			# Define a data bloc with a fixed size given by 'header_length' parameter
-			# the default value for 'header_length' (4096) is given in the header of this file
-			# the lines begining with '@param' are interpreted by the parsor
-			( header $(header_length)              
-
-				"{\n"
-				'b' edf_header
-				'b' specific_metadata
-				# padding pattern (default is a 80 blank spaces string terminating with a CR)
-				...
-				"\n}\n"
-			)
-
-			# Define output as binary file
-			b> $(dir)/$(image_full_name).edf
-
-			# Output header bloc as binary data
-			'b' header
-			# Output data bloc as binary data
-			'b' binarydata
-			
-		?)
-		
-	@)
-	
-@)
+#==============================================================================
+# File: 
+#	Multiframes_to_EDF.nxe
+#
+# @desc	Produce a EDF (ESRF Data Format) file for each image captured in 'multiframe' CCD camera mode
+#
+# @param dir directory 'Target directory for extracted data' $(_data_extraction_folder_)
+# @param header_length number 'EDF file header length' 4096
+#
+# Usage:
+#	nxextractor -t Multiframes_to_EDF.nxe -D dir=<destination directory> [-m <mode>] [-w uid:gid] <NeXus source file>
+#
+# $Author: poirier $
+#
+# $Revision: 1.7 $
+#==============================================================================
+
+# output to console
+>
+"%s\n" $(_FILE_NAME_)
+
+# loop other all entries
+# variable $(entry) will contain current entry path (ex: '/entry1')
+# variable $(entry_name) will contain curren tentry name (ex: 'entry1')
+@( entry = [nxs:/<NXentry>/]
+
+	# loop other range [0, n[
+	@( i = 0, nxs:$(entry)<NXentry>/<NXinstrument>/<NXdetector>/Frames/data
+
+		# define a new variable
+		% image_grp = $(entry)<NXentry>/image#$(i)<NXdata>
+
+		# define image name for edf file name using a data bloc named 'image_name'
+		( image_name
+			"im_%02d" $(i)
+		)
+
+		# define variable
+		% image_full_name = $(entry_name)_$(image_name)
+
+		# Test data dimensions
+		?( nxs:$(image_grp)/<SDS-signal>._rank_ = 2
+
+			# Define data bloc for image data
+			( binarydata
+				# output into this bloc as 2 bytes unsigned integers
+				'ui2' nxs:$(image_grp)/<SDS-signal> 
+			)
+
+			# Define data bloc in memory for EDF header base content
+			( edf_header
+
+				"EDF_DataBlockID = 1.Image.Psd ;\n"
+				"EDF_BinarySize = %s ;\n" $(binarydata_size)
+				"EDF_HeaderSize = %s ;\n" $(header_length)
+				"ByteOrder = LowByteFirst ;\n"
+				"DataType = UnsignedShort ;\n"
+				"Dim_1 = %d ;\n" nxs:$(image_grp)/data._size_(1)
+				"Dim_2 = %d ;\n" nxs:$(image_grp)/data._size_(2)
+				"Title = %s ;\n" $(image_full_name)
+				"Time =  ;\n"
+				"HeaderID = EH:000001:000000:000000 ;\n"
+				"Compression = None ;\n"
+				"Image = 1 ;\n"
+				"Size = %s ;\n" $(binarydata_size)
+			)
+
+			# Define data bloc for specific metadata
+			( specific_metadata
+				# loop other all NXintensity_monitor groups inside first (and unique) NXinstrument group
+				@( mi_channel = [nxs:$(entry)/<NXinstrument>/<NXintensity_monitor>]
+					"Intensity(%s) = %g ;\n" $(mi_channel_name), nxs:$(mi_channel)/intensity[i]
+					"Gain(%s) = %g ;\n" $(mi_channel_name), nxs:$(mi_channel)/Gain/data
+					"Offset(%s) = %g ;\n" $(mi_channel_name), nxs:$(mi_channel)/offset/data
+				@)
+
+				"Machine_Current = %? ;\n" nxs:$(entry)/<NXinstrument>/<NXsource>/current
+				"Monochromator_energy = %?%s ;\n" nxs:$(entry)/<NXinstrument>/<NXmonochromator>/energy, nxs:$(entry)/<NXinstrument>/<NXmonochromator>/energy.units
+				"Distance_sample-detector = %?mm ;\n" nxs:$(entry)/<NXinstrument>/<NXdetector>/distance
+
+				# aviex parameters
+				"_diffrn_detector.detector = %s ;\n" nxs:$(entry)/<NXinstrument>/<NXdetector>/type
+				"Exposure_time  = %?%s ;\n" nxs:$(entry)/<NXinstrument>/<NXdetector>/Exposure/data, nxs:$(entry)/<NXinstrument>/<NXdetector>/Exposure/data.units
+				"Shutter_close_delay  = %?%s ;\n" nxs:$(entry)/<NXinstrument>/<NXdetector>/ShutterCloseDelay/data, nxs:$(entry)/<NXinstrument>/<NXdetector>/ShutterCloseDelay/data.units
+				"Xbin = %? ;\n" nxs:$(entry)/<NXinstrument>/<NXdetector>/Xbin/data
+				"Ybin = %? ;\n" nxs:$(entry)/<NXinstrument>/<NXdetector>/Ybin/data
+
+				# motors
+				@( motor_data = [nxs:$(entry)/<NXinstrument>/<NXpositioner>]
+					"Position(%s) = %g ;\n" $(motor_data_name), nxs:$(motor_data)/raw_value
+				@)
+			)
+
+			# Define a data bloc with a fixed size given by 'header_length' parameter
+			# the default value for 'header_length' (4096) is given in the header of this file
+			# the lines begining with '@param' are interpreted by the parsor
+			( header $(header_length)              
+
+				"{\n"
+				'b' edf_header
+				'b' specific_metadata
+				# padding pattern (default is a 80 blank spaces string terminating with a CR)
+				...
+				"\n}\n"
+			)
+
+			# Define output as binary file
+			b> $(dir)/$(image_full_name).edf
+
+			# Output header bloc as binary data
+			'b' header
+			# Output data bloc as binary data
+			'b' binarydata
+
+		?)
+
+	@)
+
+@)
diff --git a/contrib/applications/NXextract/example/template_3.nxe b/contrib/applications/NXextract/example/template_3.nxe
@@ -1,66 +1,66 @@
-#==============================================================================
-# File: 
-#	scan1D_bmp_raw.nxe
-#
-# @desc	Bmp and raw data extractor. Extract 2D data (images) from 1D scan
-#
-# @param dir directory 'Target directory for extracted data' $(_data_extraction_folder_)
-
-# @usage
-#	nxextractor -t scan1D_bmp_raw.nxe -D dir=<destination_directory> [-m <mode>] [-w uid:gid] <NeXus source file>
-#
-# $Author: poirier $
-#
-# $Revision: 1.6 $
-#==============================================================================
-
-# Loop over NXentry groups.
-# Variables 'entry_name' and 'entry' will respectively contains the name and the full path of
-# the current NXentry group
-@( entry = [nxs:/<NXentry>/]
-
-	# define a variable
-	% datagrp = $(entry_name)<NXentry>/scan_data<NXdata>
-
-	# define output file in ASCII mode
-	> $(dir)/$(_FILE_NAME_)_$(entry_name).txt
-
-	# output some text data
-	"# NeXus source file: $(_FILE_NAME_)\n"
-	"# Creation time: %?\n" nxs:.file_time
-	"# NXentry: name = %s\n" $(entry_name)
-	"\n"
-
-	# Loop over datasets containing the 'signal' attribute in the NXdata group
-	@( signal = [nxs:/$(datagrp)/<SDS-signal>]
-
-		# Checking dataset rank
-		?( nxs:$(signal)._rank_ = 3
-
-			# loop over actuators arrays dimension
-			@( i = 0, nxs:/$(signal)._size_(1)
-	  
-				# defining a data bloc in memory
-				( output_filename
-					"%04d-" $(i)
-					"%6.3f" nxs:/$(datagrp)/<SDS-axis1>[i]
-				)
-
-				# Re-define output in binary mode
-				# the content of the variable 'dir' is passed through a argument of the command line
-				# the content of the variable 'output_filename' is defining by the data bloc above
-				b> $(dir)/$(entry_name)/$(output_filename).bmp
-
-				# output 2D data slice of 3D array as a bmp image
-				'bmp' nxs:/$(signal)[i]
-
-				# Re-define output
-				b> $(dir)/$(entry_name)/$(output_filename).raw
-
-				# output same data as a binary bloc of 2 bytes integers
-				'i2' nxs:/$(signal)[i]
-
-			@)
-		?)
-	@)
-@)
+#==============================================================================
+# File: 
+#	scan1D_bmp_raw.nxe
+#
+# @desc	Bmp and raw data extractor. Extract 2D data (images) from 1D scan
+#
+# @param dir directory 'Target directory for extracted data' $(_data_extraction_folder_)
+
+# @usage
+#	nxextractor -t scan1D_bmp_raw.nxe -D dir=<destination_directory> [-m <mode>] [-w uid:gid] <NeXus source file>
+#
+# $Author: poirier $
+#
+# $Revision: 1.6 $
+#==============================================================================
+
+# Loop over NXentry groups.
+# Variables 'entry_name' and 'entry' will respectively contains the name and the full path of
+# the current NXentry group
+@( entry = [nxs:/<NXentry>/]
+
+	# define a variable
+	% datagrp = $(entry_name)<NXentry>/scan_data<NXdata>
+
+	# define output file in ASCII mode
+	> $(dir)/$(_FILE_NAME_)_$(entry_name).txt
+
+	# output some text data
+	"# NeXus source file: $(_FILE_NAME_)\n"
+	"# Creation time: %?\n" nxs:.file_time
+	"# NXentry: name = %s\n" $(entry_name)
+	"\n"
+
+	# Loop over datasets containing the 'signal' attribute in the NXdata group
+	@( signal = [nxs:/$(datagrp)/<SDS-signal>]
+
+		# Checking dataset rank
+		?( nxs:$(signal)._rank_ = 3
+
+			# loop over actuators arrays dimension
+			@( i = 0, nxs:/$(signal)._size_(1)
+
+				# defining a data bloc in memory
+				( output_filename
+					"%04d-" $(i)
+					"%6.3f" nxs:/$(datagrp)/<SDS-axis1>[i]
+				)
+
+				# Re-define output in binary mode
+				# the content of the variable 'dir' is passed through a argument of the command line
+				# the content of the variable 'output_filename' is defining by the data bloc above
+				b> $(dir)/$(entry_name)/$(output_filename).bmp
+
+				# output 2D data slice of 3D array as a bmp image
+				'bmp' nxs:/$(signal)[i]
+
+				# Re-define output
+				b> $(dir)/$(entry_name)/$(output_filename).raw
+
+				# output same data as a binary bloc of 2 bytes integers
+				'i2' nxs:/$(signal)[i]
+
+			@)
+		?)
+	@)
+@)