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FreddieAkeroydFreddieAkeroyd
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Normalise line endings
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Lines changed: 17986 additions & 17986 deletions

‎cmake_include/FindJNI.cmake‎

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‎cmake_include/FindJava.cmake‎

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‎cmake_include/Utilities.cmake‎

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‎contrib/applications/NXextract/example/template_1.nxe‎

Lines changed: 119 additions & 119 deletions
Original file line numberDiff line numberDiff line change
@@ -1,119 +1,119 @@
1-
#==============================================================================
2-
# File:
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# Multiframes_to_EDF.nxe
4-
#
5-
# @desc Produce a EDF (ESRF Data Format) file for each image captured in 'multiframe' CCD camera mode
6-
#
7-
# @param dir directory 'Target directory for extracted data' $(_data_extraction_folder_)
8-
# @param header_length number 'EDF file header length' 4096
9-
#
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# Usage:
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# nxextractor -t Multiframes_to_EDF.nxe -D dir=<destination directory> [-m <mode>] [-w uid:gid] <NeXus source file>
12-
#
13-
# $Author: poirier $
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#
15-
# $Revision: 1.7 $
16-
#==============================================================================
17-
18-
# output to console
19-
>
20-
"%s\n" $(_FILE_NAME_)
21-
22-
# loop other all entries
23-
# variable $(entry) will contain current entry path (ex: '/entry1')
24-
# variable $(entry_name) will contain curren tentry name (ex: 'entry1')
25-
@( entry = [nxs:/<NXentry>/]
26-
27-
# loop other range [0, n[
28-
@( i = 0, nxs:$(entry)<NXentry>/<NXinstrument>/<NXdetector>/Frames/data
29-
30-
# define a new variable
31-
% image_grp = $(entry)<NXentry>/image#$(i)<NXdata>
32-
33-
# define image name for edf file name using a data bloc named 'image_name'
34-
( image_name
35-
"im_%02d" $(i)
36-
)
37-
38-
# define variable
39-
% image_full_name = $(entry_name)_$(image_name)
40-
41-
# Test data dimensions
42-
?( nxs:$(image_grp)/<SDS-signal>._rank_ = 2
43-
44-
# Define data bloc for image data
45-
( binarydata
46-
# output into this bloc as 2 bytes unsigned integers
47-
'ui2' nxs:$(image_grp)/<SDS-signal>
48-
)
49-
50-
# Define data bloc in memory for EDF header base content
51-
( edf_header
52-
53-
"EDF_DataBlockID = 1.Image.Psd ;\n"
54-
"EDF_BinarySize = %s ;\n" $(binarydata_size)
55-
"EDF_HeaderSize = %s ;\n" $(header_length)
56-
"ByteOrder = LowByteFirst ;\n"
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"DataType = UnsignedShort ;\n"
58-
"Dim_1 = %d ;\n" nxs:$(image_grp)/data._size_(1)
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"Dim_2 = %d ;\n" nxs:$(image_grp)/data._size_(2)
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"Title = %s ;\n" $(image_full_name)
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"Time = ;\n"
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"HeaderID = EH:000001:000000:000000 ;\n"
63-
"Compression = None ;\n"
64-
"Image = 1 ;\n"
65-
"Size = %s ;\n" $(binarydata_size)
66-
)
67-
68-
# Define data bloc for specific metadata
69-
( specific_metadata
70-
# loop other all NXintensity_monitor groups inside first (and unique) NXinstrument group
71-
@( mi_channel = [nxs:$(entry)/<NXinstrument>/<NXintensity_monitor>]
72-
"Intensity(%s) = %g ;\n" $(mi_channel_name), nxs:$(mi_channel)/intensity[i]
73-
"Gain(%s) = %g ;\n" $(mi_channel_name), nxs:$(mi_channel)/Gain/data
74-
"Offset(%s) = %g ;\n" $(mi_channel_name), nxs:$(mi_channel)/offset/data
75-
@)
76-
77-
"Machine_Current = %? ;\n" nxs:$(entry)/<NXinstrument>/<NXsource>/current
78-
"Monochromator_energy = %?%s ;\n" nxs:$(entry)/<NXinstrument>/<NXmonochromator>/energy, nxs:$(entry)/<NXinstrument>/<NXmonochromator>/energy.units
79-
"Distance_sample-detector = %?mm ;\n" nxs:$(entry)/<NXinstrument>/<NXdetector>/distance
80-
81-
# aviex parameters
82-
"_diffrn_detector.detector = %s ;\n" nxs:$(entry)/<NXinstrument>/<NXdetector>/type
83-
"Exposure_time = %?%s ;\n" nxs:$(entry)/<NXinstrument>/<NXdetector>/Exposure/data, nxs:$(entry)/<NXinstrument>/<NXdetector>/Exposure/data.units
84-
"Shutter_close_delay = %?%s ;\n" nxs:$(entry)/<NXinstrument>/<NXdetector>/ShutterCloseDelay/data, nxs:$(entry)/<NXinstrument>/<NXdetector>/ShutterCloseDelay/data.units
85-
"Xbin = %? ;\n" nxs:$(entry)/<NXinstrument>/<NXdetector>/Xbin/data
86-
"Ybin = %? ;\n" nxs:$(entry)/<NXinstrument>/<NXdetector>/Ybin/data
87-
88-
# motors
89-
@( motor_data = [nxs:$(entry)/<NXinstrument>/<NXpositioner>]
90-
"Position(%s) = %g ;\n" $(motor_data_name), nxs:$(motor_data)/raw_value
91-
@)
92-
)
93-
94-
# Define a data bloc with a fixed size given by 'header_length' parameter
95-
# the default value for 'header_length' (4096) is given in the header of this file
96-
# the lines begining with '@param' are interpreted by the parsor
97-
( header $(header_length)
98-
99-
"{\n"
100-
'b' edf_header
101-
'b' specific_metadata
102-
# padding pattern (default is a 80 blank spaces string terminating with a CR)
103-
...
104-
"\n}\n"
105-
)
106-
107-
# Define output as binary file
108-
b> $(dir)/$(image_full_name).edf
109-
110-
# Output header bloc as binary data
111-
'b' header
112-
# Output data bloc as binary data
113-
'b' binarydata
114-
115-
?)
116-
117-
@)
118-
119-
@)
1+
#==============================================================================
2+
# File:
3+
# Multiframes_to_EDF.nxe
4+
#
5+
# @desc Produce a EDF (ESRF Data Format) file for each image captured in 'multiframe' CCD camera mode
6+
#
7+
# @param dir directory 'Target directory for extracted data' $(_data_extraction_folder_)
8+
# @param header_length number 'EDF file header length' 4096
9+
#
10+
# Usage:
11+
# nxextractor -t Multiframes_to_EDF.nxe -D dir=<destination directory> [-m <mode>] [-w uid:gid] <NeXus source file>
12+
#
13+
# $Author: poirier $
14+
#
15+
# $Revision: 1.7 $
16+
#==============================================================================
17+
18+
# output to console
19+
>
20+
"%s\n" $(_FILE_NAME_)
21+
22+
# loop other all entries
23+
# variable $(entry) will contain current entry path (ex: '/entry1')
24+
# variable $(entry_name) will contain curren tentry name (ex: 'entry1')
25+
@( entry = [nxs:/<NXentry>/]
26+
27+
# loop other range [0, n[
28+
@( i = 0, nxs:$(entry)<NXentry>/<NXinstrument>/<NXdetector>/Frames/data
29+
30+
# define a new variable
31+
% image_grp = $(entry)<NXentry>/image#$(i)<NXdata>
32+
33+
# define image name for edf file name using a data bloc named 'image_name'
34+
( image_name
35+
"im_%02d" $(i)
36+
)
37+
38+
# define variable
39+
% image_full_name = $(entry_name)_$(image_name)
40+
41+
# Test data dimensions
42+
?( nxs:$(image_grp)/<SDS-signal>._rank_ = 2
43+
44+
# Define data bloc for image data
45+
( binarydata
46+
# output into this bloc as 2 bytes unsigned integers
47+
'ui2' nxs:$(image_grp)/<SDS-signal>
48+
)
49+
50+
# Define data bloc in memory for EDF header base content
51+
( edf_header
52+
53+
"EDF_DataBlockID = 1.Image.Psd ;\n"
54+
"EDF_BinarySize = %s ;\n" $(binarydata_size)
55+
"EDF_HeaderSize = %s ;\n" $(header_length)
56+
"ByteOrder = LowByteFirst ;\n"
57+
"DataType = UnsignedShort ;\n"
58+
"Dim_1 = %d ;\n" nxs:$(image_grp)/data._size_(1)
59+
"Dim_2 = %d ;\n" nxs:$(image_grp)/data._size_(2)
60+
"Title = %s ;\n" $(image_full_name)
61+
"Time = ;\n"
62+
"HeaderID = EH:000001:000000:000000 ;\n"
63+
"Compression = None ;\n"
64+
"Image = 1 ;\n"
65+
"Size = %s ;\n" $(binarydata_size)
66+
)
67+
68+
# Define data bloc for specific metadata
69+
( specific_metadata
70+
# loop other all NXintensity_monitor groups inside first (and unique) NXinstrument group
71+
@( mi_channel = [nxs:$(entry)/<NXinstrument>/<NXintensity_monitor>]
72+
"Intensity(%s) = %g ;\n" $(mi_channel_name), nxs:$(mi_channel)/intensity[i]
73+
"Gain(%s) = %g ;\n" $(mi_channel_name), nxs:$(mi_channel)/Gain/data
74+
"Offset(%s) = %g ;\n" $(mi_channel_name), nxs:$(mi_channel)/offset/data
75+
@)
76+
77+
"Machine_Current = %? ;\n" nxs:$(entry)/<NXinstrument>/<NXsource>/current
78+
"Monochromator_energy = %?%s ;\n" nxs:$(entry)/<NXinstrument>/<NXmonochromator>/energy, nxs:$(entry)/<NXinstrument>/<NXmonochromator>/energy.units
79+
"Distance_sample-detector = %?mm ;\n" nxs:$(entry)/<NXinstrument>/<NXdetector>/distance
80+
81+
# aviex parameters
82+
"_diffrn_detector.detector = %s ;\n" nxs:$(entry)/<NXinstrument>/<NXdetector>/type
83+
"Exposure_time = %?%s ;\n" nxs:$(entry)/<NXinstrument>/<NXdetector>/Exposure/data, nxs:$(entry)/<NXinstrument>/<NXdetector>/Exposure/data.units
84+
"Shutter_close_delay = %?%s ;\n" nxs:$(entry)/<NXinstrument>/<NXdetector>/ShutterCloseDelay/data, nxs:$(entry)/<NXinstrument>/<NXdetector>/ShutterCloseDelay/data.units
85+
"Xbin = %? ;\n" nxs:$(entry)/<NXinstrument>/<NXdetector>/Xbin/data
86+
"Ybin = %? ;\n" nxs:$(entry)/<NXinstrument>/<NXdetector>/Ybin/data
87+
88+
# motors
89+
@( motor_data = [nxs:$(entry)/<NXinstrument>/<NXpositioner>]
90+
"Position(%s) = %g ;\n" $(motor_data_name), nxs:$(motor_data)/raw_value
91+
@)
92+
)
93+
94+
# Define a data bloc with a fixed size given by 'header_length' parameter
95+
# the default value for 'header_length' (4096) is given in the header of this file
96+
# the lines begining with '@param' are interpreted by the parsor
97+
( header $(header_length)
98+
99+
"{\n"
100+
'b' edf_header
101+
'b' specific_metadata
102+
# padding pattern (default is a 80 blank spaces string terminating with a CR)
103+
...
104+
"\n}\n"
105+
)
106+
107+
# Define output as binary file
108+
b> $(dir)/$(image_full_name).edf
109+
110+
# Output header bloc as binary data
111+
'b' header
112+
# Output data bloc as binary data
113+
'b' binarydata
114+
115+
?)
116+
117+
@)
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119+
@)

‎contrib/applications/NXextract/example/template_3.nxe‎

Lines changed: 66 additions & 66 deletions
Original file line numberDiff line numberDiff line change
@@ -1,66 +1,66 @@
1-
#==============================================================================
2-
# File:
3-
# scan1D_bmp_raw.nxe
4-
#
5-
# @desc Bmp and raw data extractor. Extract 2D data (images) from 1D scan
6-
#
7-
# @param dir directory 'Target directory for extracted data' $(_data_extraction_folder_)
8-
9-
# @usage
10-
# nxextractor -t scan1D_bmp_raw.nxe -D dir=<destination_directory> [-m <mode>] [-w uid:gid] <NeXus source file>
11-
#
12-
# $Author: poirier $
13-
#
14-
# $Revision: 1.6 $
15-
#==============================================================================
16-
17-
# Loop over NXentry groups.
18-
# Variables 'entry_name' and 'entry' will respectively contains the name and the full path of
19-
# the current NXentry group
20-
@( entry = [nxs:/<NXentry>/]
21-
22-
# define a variable
23-
% datagrp = $(entry_name)<NXentry>/scan_data<NXdata>
24-
25-
# define output file in ASCII mode
26-
> $(dir)/$(_FILE_NAME_)_$(entry_name).txt
27-
28-
# output some text data
29-
"# NeXus source file: $(_FILE_NAME_)\n"
30-
"# Creation time: %?\n" nxs:.file_time
31-
"# NXentry: name = %s\n" $(entry_name)
32-
"\n"
33-
34-
# Loop over datasets containing the 'signal' attribute in the NXdata group
35-
@( signal = [nxs:/$(datagrp)/<SDS-signal>]
36-
37-
# Checking dataset rank
38-
?( nxs:$(signal)._rank_ = 3
39-
40-
# loop over actuators arrays dimension
41-
@( i = 0, nxs:/$(signal)._size_(1)
42-
43-
# defining a data bloc in memory
44-
( output_filename
45-
"%04d-" $(i)
46-
"%6.3f" nxs:/$(datagrp)/<SDS-axis1>[i]
47-
)
48-
49-
# Re-define output in binary mode
50-
# the content of the variable 'dir' is passed through a argument of the command line
51-
# the content of the variable 'output_filename' is defining by the data bloc above
52-
b> $(dir)/$(entry_name)/$(output_filename).bmp
53-
54-
# output 2D data slice of 3D array as a bmp image
55-
'bmp' nxs:/$(signal)[i]
56-
57-
# Re-define output
58-
b> $(dir)/$(entry_name)/$(output_filename).raw
59-
60-
# output same data as a binary bloc of 2 bytes integers
61-
'i2' nxs:/$(signal)[i]
62-
63-
@)
64-
?)
65-
@)
66-
@)
1+
#==============================================================================
2+
# File:
3+
# scan1D_bmp_raw.nxe
4+
#
5+
# @desc Bmp and raw data extractor. Extract 2D data (images) from 1D scan
6+
#
7+
# @param dir directory 'Target directory for extracted data' $(_data_extraction_folder_)
8+
9+
# @usage
10+
# nxextractor -t scan1D_bmp_raw.nxe -D dir=<destination_directory> [-m <mode>] [-w uid:gid] <NeXus source file>
11+
#
12+
# $Author: poirier $
13+
#
14+
# $Revision: 1.6 $
15+
#==============================================================================
16+
17+
# Loop over NXentry groups.
18+
# Variables 'entry_name' and 'entry' will respectively contains the name and the full path of
19+
# the current NXentry group
20+
@( entry = [nxs:/<NXentry>/]
21+
22+
# define a variable
23+
% datagrp = $(entry_name)<NXentry>/scan_data<NXdata>
24+
25+
# define output file in ASCII mode
26+
> $(dir)/$(_FILE_NAME_)_$(entry_name).txt
27+
28+
# output some text data
29+
"# NeXus source file: $(_FILE_NAME_)\n"
30+
"# Creation time: %?\n" nxs:.file_time
31+
"# NXentry: name = %s\n" $(entry_name)
32+
"\n"
33+
34+
# Loop over datasets containing the 'signal' attribute in the NXdata group
35+
@( signal = [nxs:/$(datagrp)/<SDS-signal>]
36+
37+
# Checking dataset rank
38+
?( nxs:$(signal)._rank_ = 3
39+
40+
# loop over actuators arrays dimension
41+
@( i = 0, nxs:/$(signal)._size_(1)
42+
43+
# defining a data bloc in memory
44+
( output_filename
45+
"%04d-" $(i)
46+
"%6.3f" nxs:/$(datagrp)/<SDS-axis1>[i]
47+
)
48+
49+
# Re-define output in binary mode
50+
# the content of the variable 'dir' is passed through a argument of the command line
51+
# the content of the variable 'output_filename' is defining by the data bloc above
52+
b> $(dir)/$(entry_name)/$(output_filename).bmp
53+
54+
# output 2D data slice of 3D array as a bmp image
55+
'bmp' nxs:/$(signal)[i]
56+
57+
# Re-define output
58+
b> $(dir)/$(entry_name)/$(output_filename).raw
59+
60+
# output same data as a binary bloc of 2 bytes integers
61+
'i2' nxs:/$(signal)[i]
62+
63+
@)
64+
?)
65+
@)
66+
@)

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