From 7eca6719bed13dc5366c92da6298f1355d10c044 Mon Sep 17 00:00:00 2001 From: Jerome Kieffer Date: Fri, 6 Feb 2015 11:35:59 +0100 Subject: [PATCH] update documentation --- doc/source/performances.rst | 2 +- fabio-src/binaryimage.py | 7 ++++--- fabio-src/cbfimage.py | 6 +++--- fabio-src/compression.py | 1 + fabio-src/mar345image.py | 7 +++++-- test/all_testimages.json | 28 ++++++++++++++-------------- 6 files changed, 28 insertions(+), 23 deletions(-) diff --git a/doc/source/performances.rst b/doc/source/performances.rst index 1065b0812..8ca00d292 100644 --- a/doc/source/performances.rst +++ b/doc/source/performances.rst @@ -4,7 +4,7 @@ Benchmarks Those benchmarks have been done with all data already in cache using a Intel Xeon E5520 @ 2.27GHz running Debian 7. -.. table:: Execution time for reading a file, benchmarked using the ``timeit'' module. :label:`Benchmark` +.. table:: Execution time for reading a file, benchmarked using the ``timeit'' module. :class: w +---------------+---------------------------+--------+--------------+--------------+--------------+ diff --git a/fabio-src/binaryimage.py b/fabio-src/binaryimage.py index 166294694..6a15bd8ba 100644 --- a/fabio-src/binaryimage.py +++ b/fabio-src/binaryimage.py @@ -2,6 +2,7 @@ # coding: utf-8 """ Authors: Gael Goret, Jerome Kieffer, ESRF, France + Emails: gael.goret@esrf.fr, jerome.kieffer@esrf.fr Brian Richard Pauw @@ -28,8 +29,8 @@ class binaryimage(fabioimage): """ This simple library has been made for manipulating exotic/unknown files format. - Binary files images are simple none-compressed 2D images only defined by their : - data-type, dimensions, byte order and offset + Binary files images are simple none-compressed 2D images only defined by their: + data-type, dimensions, byte order and offset if offset is set to a negative value, the image is read using the last data but n data in the file, skipping any header. @@ -74,7 +75,7 @@ def read(self, fname, dim1, dim2, offset=0, bytecode="int32", endian="<"): f.seek(offset) else: try: - f.seek(-size + offset + 1, 2) #seek from EOF backwards + f.seek(-size + offset + 1, 2) # seek from EOF backwards except IOError: logging.warn('expected datablock too large, please check bytecode settings: {}'.format(bytecode)) except: diff --git a/fabio-src/cbfimage.py b/fabio-src/cbfimage.py index 5f7f95620..1f97be50c 100644 --- a/fabio-src/cbfimage.py +++ b/fabio-src/cbfimage.py @@ -17,7 +17,7 @@ __author__ = "Jérôme Kieffer" __contact__ = "jerome.kieffer@esrf.eu" __license__ = "GPLv3+" -__date__ = "19/01/2015" +__date__ = "06/02/2015" __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" __version__ = ["Generated by CIF.py: Jan 2005 - April 2012", "Written by Jerome Kieffer: Jerome.Kieffer@esrf.eu", @@ -643,6 +643,7 @@ def saveCIF(self, _strFilename="test.cif", linesep=os.linesep, binary=False): @param _strFilename: the of the file to be written @param linesep: line separation used (to force compatibility with windows/unix) @param binary: Shall we write the data as binary (True only for imageCIF/CBF) + @return: None """ if binary: mode = "wb" @@ -667,10 +668,9 @@ def tostring(self, _strFilename=None, linesep=os.linesep): @param _strFilename: the name of the filename to be appended in the header of the CIF file @type _strFilename: string @param linesep: default line separation: can be "\n" or "\r\n" - @return: a sting that corresponds to the content of the CIF - file. + @return: a string that corresponds to the content of the CIF-file. """ -# sCifText = "" lstStrCif = ["# " + i for i in __version__] if "_chemical_name_common" in self: t = self["_chemical_name_common"].split()[0] diff --git a/fabio-src/compression.py b/fabio-src/compression.py index d1f20a471..04b49c3c1 100644 --- a/fabio-src/compression.py +++ b/fabio-src/compression.py @@ -322,6 +322,7 @@ def decPCK(stream, dim1=None, dim2=None, overflowPix=None, version=None, normal_ @param normal_start: position of the normal value section (can be auto-guessed) @param swap_needed: set to True when reading data from a foreign endianness (little on big or big on little) @return : ndarray of 2D with the right size + """ try: from .mar345_IO import uncompress_pck diff --git a/fabio-src/mar345image.py b/fabio-src/mar345image.py index 3b77002f7..cb122281b 100644 --- a/fabio-src/mar345image.py +++ b/fabio-src/mar345image.py @@ -23,7 +23,7 @@ from __future__ import with_statement, print_function, absolute_import __authors__ = ["Henning O. Sorensen" , "Erik Knudsen", "Jon Wright", "Jérôme Kieffer"] -__date__ = "04/02/2015" +__date__ = "06/02/2015" __status__ = "production" __copyright__ = "2007-2009 Risoe National Laboratory; 2010-2015 ESRF" __licence__ = "GPL" @@ -211,9 +211,12 @@ def binary_header(self): def ascii_header(self, linesep="\n", size=4096): """ + Generate the ASCII header for writing + @param linesep: end of line separator @param size: size of the header (without the binary header) - @return string (unicode) containing the mar345 header + @return: string (unicode) containing the mar345 header + """ try: version = sys.modules["fabio"].version diff --git a/test/all_testimages.json b/test/all_testimages.json index e6dd98124..722b8c6f5 100644 --- a/test/all_testimages.json +++ b/test/all_testimages.json @@ -16,11 +16,11 @@ "i01f0001.edf.bz2", "a0009.tif.bz2", "GE_aSI_detector_image_1529.gz", - "corkcont2_H_0089.mccd", + "Cr8F8140k103.0026.bz2", "face.msk.bz2", "b191_1_9_1.img", "id13_badPadding.edf", - "a0009.edf.bz2", + "b191_1_9_1.img.bz2", "example.mar2300.gz", "a0009.tif", "MultiFrame.edf.bz2", @@ -42,35 +42,35 @@ "d80_60s.img.gz", "oPPA_5grains_0001.tif.gz", "b191_1_9_1_uncompressed.img.bz2", - "pilatus2M.edf", + "F2K_Seb_Lyso0675.edf", "somedata_0001.mccd.bz2", - "MultiFrame-Frame0.edf", + "MultiFrame-Frame0.edf.bz2", "fit2d.tif", "a0009.tif.gz", - "oPPA_5grains_0001.edf.bz2", + "edfUncompressed_U16.edf.bz2", "run2_1_00148.cbf", "mb_LP_1_001.edf", "face.edf", "face.msk.gz", "mb_LP_1_001.img.bz2", "F2K_Seb_Lyso0675_header_only.edf.bz2", - "F2K_Seb_Lyso0675.edf", + "pilatus2M.edf", "testmap1_0002.tif", "testmap1_0002.tif.bz2", "face.edf.gz", "F2K_Seb_Lyso0675.edf.gz", "edfUncompressed_U16.edf.gz", "edfGzip_U16.edf.bz2", - "i01f0001.edf", + "id13_badPadding.edf.gz", "edfGzip_U16.edf.gz", "XSDataImage.xml", "XSDataImage.edf.gz", "XSDataImage.xml.gz", - "run2_1_00148.edf", + "Fe3O4_023_101.mar2560.gz", "fit2d_click.edf.gz", "Fe3O4_023_101.mar2560.bz2", "fit2d.tif.gz", - "MultiFrame-Frame0.edf.bz2", + "MultiFrame-Frame0.edf", "somedata_0001.mccd.gz", "somedata_0001.mccd", "run2_1_00148.edf.gz", @@ -95,12 +95,12 @@ "d80_60s.edf.gz", "a0009.edf", "XSDataImage.edf.bz2", - "edfUncompressed_U16.edf.bz2", + "oPPA_5grains_0001.edf.bz2", "pilatus2M.edf.bz2", "fit2d.edf.bz2", "Cr8F8140k103.0026.gz", "GE_aSI_detector_image_1529", - "Fe3O4_023_101.mar2560.gz", + "run2_1_00148.edf", "mgzn-20hpt.img", "MultiFrame.edf", "fit2d_click.edf", @@ -110,8 +110,8 @@ "MultiFrame-Frame0.edf.gz", "run2_1_00148.edf.bz2", "fit2d.tif.bz2", - "Cr8F8140k103.0026.bz2", - "b191_1_9_1.img.bz2", + "corkcont2_H_0089.mccd", + "a0009.edf.bz2", "pilatus2M.tif.gz", "i01f0001.edf.gz", "image0001.pgm.gz", @@ -119,7 +119,7 @@ "example.mar2300", "mgzn-20hpt.img.gz", "MultiFrame.edf.gz", - "id13_badPadding.edf.gz", + "i01f0001.edf", "i01f0001.kcd.gz", "XSDataImageInv.xml", "b191_1_9_1_uncompressed.img",