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--- xray_data:convertfileseries [2019/01/18 14:19] – created smerkel
+++ xray_data:convertfileseries [2026/08/10 10:37] (current) – smerkel
@@ Line 1: / Line 1: @@
-Convert!
+====== Convert image file series ======
+===== Introduction =====
+Typical diamond anvil cell beamlines generate series of diffraction files in various formats, which are not the [[fileformat:edf|EDF]] format used in further processing. The tools here can be used to convert the files into the proper format.
+Data collected at step scans have a starting ω position, an end ω position, and a step size δω. Diffraction are collected at each ω and save in files such as ''name-0000.tif'', ''name-0001.tif'', etc. For instance, if you collect data from -2° to +2° with a step size of 1.0°, starting from image 5, with a stem ''mydata'', you will save the following data files
+  * ''mydata-0005.tif'' for a scan between ω = -2.0° to -1.0° with an average ω of -1.5°,
+  * ''mydata-0006.tif'' for a scan between ω = -1.0° to -0.0° with an average ω of -0.5°,
+  * ''mydata-0007.tif'' for a scan between ω = +0.0° to +1.0° with an average ω of -0.5°,
+  * ''mydata-0008.tif'' for a scan between ω = +1.0° to +2.0° with an average ω of -1.5°.
+The scripts ''timelessTiff2edf'' and ''timelessMccd2edf'', which are both part of the [[software:timelesstools|TIMEleSS tools]], are meant to convert such file series into series of EDF files.
+Watch out! You can generate vast amount of data! You may want to include such scripts into larger scripts as you develop your data processing strategy.
+===== timelessTiff2edf =====
+<code>
+timelessTiff2edf -h
+usage: timelessTiff2edf -f from -t to -s step -n stem -i first image [OPTIONS]
+Creates a list of EDF files based on a collection of TIFF files This is part
+of the TIMEleSS project http://timeless.texture.rocks
+optional arguments:
+  -h, --help            show this help message and exit
+  -f FROM, --from FROM  Start for omega scan (in degrees, required)
+  -t TO, --to TO        End for omega scan (in degrees, required)
+  -s STEP, --step STEP  Omega step (in degrees, required)
+  -n STEM, --stem STEM  Stem for images files (required)
+  -i IMAGEFIRST, --imagefirst IMAGEFIRST
+                        Number of first image file in series (required)
+  -p TIFFIMAGEPATH, --tiffimagepath TIFFIMAGEPATH
+                        Path to tiff images. Default is ./
+  -e EDFIMAGEPATH, --edfimagepath EDFIMAGEPATH
+                        Path in which to save edf images. Default is ./
+  -x EXTENSION, --extension EXTENSION
+                        Extension for tiff files. Default is tif
+  -d NDIGITS, --ndigits NDIGITS
+                        Number of digits for file number. Default is 4
+</code>
+===== timelessMccd2edf =====
+<code>
+timelessMccd2edf -h
+usage: timelessMccd2edf -f from -t to -s step -n stem -i first image [OPTIONS]
+Creates a list of EDF files based on a collection of MarCCD files This is part
+of the TIMEleSS project http://timeless.texture.rocks
+optional arguments:
+  -h, --help            show this help message and exit
+  -f FROM, --from FROM  Start for omega scan (in degrees, required)
+  -t TO, --to TO        End for omega scan (in degrees, required)
+  -s STEP, --step STEP  Omega step (in degrees, required)
+  -n STEM, --stem STEM  Stem for images file (required)
+  -i IMAGEFIRST, --imagefirst IMAGEFIRST
+                        Number of first image file in series (required)
+  -p MCCDIMAGEPATH, --mccdimagepath MCCDIMAGEPATH
+                        Path to MarCCD images. Default is ./
+  -e EDFIMAGEPATH, --edfimagepath EDFIMAGEPATH
+                        Path in which to save edf images. Default is ./
+  -x EXTENSION, --extension EXTENSION
+                        Extension for MarCCD files. Default is mccd
+  -d NDIGITS, --ndigits NDIGITS
+                        Number of digits for file number. Default is 4
+</code>
+===== Other formats =====
+The ESRF fabio library, which you must have installed by now, can open and read many formats. Below is an example python program that will convert a series ''CBF'' files placed into a folder to ''EDF''.
+As you can see, the code is not specific to CBF, as long as Fabio can read it, it will work...
+<code>
+import glob
+import fabio, os
+cbf_dir = "/folder/with/CBFFiles"
+edf_dir = "/folder/to/save/EDFFiles"
+dest_format = "edf"
+# Starting value of omega
+omegastart = -23.5
+# Omega step
+omegastep = 0.5
+# The first file will be assigne a value of omega = omegastart+omegastep/2.
+files = glob.glob("%s/*.cbf" % cbf_dir)
+files.sort()
+print("Number of files: %s" % len(files))
+if not os.path.exists(edf_dir):
+    os.makedirs(edf_dir)
+omega = omegastart + omegastep / 2.
+for onefile in files:
+    dst_name = os.path.join(edf_dir, os.path.splitext(os.path.basename(onefile))[0] + "." + dest_format)
+    print("Converting %s into %s" % (onefile, dst_name))
+    im = fabio.open(onefile)
+    im.header["Omega"] = omega
+    im.convert(dest_format).save(dst_name)
+    omega += omegastep
+print ("Read %d file in %s" % (len(files), cbf_dir))
+print ("Saved %d file in %s"% (len(files), edf_dir))
+print ("Done")
+</code>