6197e839c9
fixed missing file extension when adding in-place
2016-03-15 14:52:10 -04:00
f857353e16
Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development
2016-03-11 12:49:47 +01:00
b0dedb8cbd
=addOrientation can do the same (and more)
2016-03-09 19:02:28 +01:00
b933359f17
clarified text of error message complaining about wrong input dimension
2016-03-09 12:28:36 -05:00
93d7643875
no long lines anymore and prospector is also happy
2016-03-03 14:44:29 +01:00
9fa49b8584
vtk files, mainly removed from vtk import *
2016-03-02 13:52:33 +01:00
e89923d6d3
next round
2016-03-02 11:11:20 +01:00
5d7e138a9b
long line
2016-03-02 10:55:21 +01:00
f77de7ac6e
adjusting style (mainly long lines an "== None")
2016-03-02 10:52:24 +01:00
043f2faeb3
line too long
2016-03-01 21:59:59 +01:00
98476ea29c
more improved scripts
2016-03-01 21:35:59 +01:00
9cfc27d295
line too long (132 lines max code, like Fortran, 159 including comments, Python standard)
2016-03-01 21:18:32 +01:00
80dc23d93d
following "prospector -t pep8 -t pyflakes -t dodgy -t profile-validator -t pep257"
2016-03-01 21:11:43 +01:00
e55d0ae3ca
further attemps to make it conform with best python practice
2016-03-01 20:44:43 +01:00
6eb170bc07
still struggling with prospector
2016-03-01 19:37:31 +01:00
3b33d320b1
getting pyflakes to ignore
2016-03-01 19:06:00 +01:00
2a50c6bf86
using prospector --tool=dodgy --tool=pyflakes -M to find python flaws
2016-03-01 18:25:14 +01:00
7c9d344601
python files now report their version depending on VERSION file in $DAMASK_ROOT
2016-01-27 17:06:00 +00:00
c710709b1a
example Makefile typically does not work, deleted
2015-12-15 14:34:03 +00:00
19ddbc9b21
fixed typo and simplified
2015-12-15 06:16:47 +00:00
d76fcb4be8
was giving wrong results
2015-12-05 21:34:39 +00:00
7eb7a4e8cd
changed to use routine for symmetric matrices as ascii table cannot handle complex number anyway. further advantage: eigvals and eigvectors will be odered
2015-12-04 22:34:19 +00:00
35202494c2
fixed issue caused by using -r twice as option label.
2015-12-04 04:33:23 +00:00
784c78a3b0
removed defunct option to output labels as column vector.
2015-12-04 04:31:53 +00:00
937634d703
added group shuffling (i.e. exchanging unique values)
2015-12-04 01:17:45 +00:00
55b33e5597
added option “inplace” to directly modify VTK file instead of creating copy_added.
2015-12-02 23:10:14 +00:00
f49091c952
addDeformedConfiguration without core module
2015-12-02 20:53:02 +00:00
0ffcb7fdaf
cleaning
2015-12-01 16:37:20 +00:00
40c2a5dd6d
differentiate name for undeformed and deformed coordinates makes sense. Still not happy with the naming though
2015-11-20 15:58:32 +00:00
4c51c15795
changed option to —coordinates.
...
gracefully extend points to be 3D.
2015-11-14 01:52:31 +00:00
2c9f9981e2
polishing of addRectiliearGridData.
...
subsumed functionality of addVoxelgridData into it.
2015-11-10 01:49:32 +00:00
ccf7530121
added output selection “rodrigues”
2015-11-10 01:34:10 +00:00
fe1dbf2ea0
output file name now contains both position and mode.
...
e.g. ${prefix}_ipinitialcoord(point).vtr
2015-11-03 21:44:36 +00:00
ad06fc1a77
fixed buggy mapIncremental behavior for anything else than averaging (the standard case luckily…)
2015-10-27 20:16:24 +00:00
ebf20f2ebc
unified style and other minor improvements
2015-10-15 19:51:27 +00:00
723f135177
can now handle tiling of values (scalar [string,number] spread out to vector and such)
2015-10-09 14:22:41 +00:00
196afb9b31
adopted change in named argument (strict -> SST) for disorientation
2015-10-09 13:06:51 +00:00
fc9d290339
unified structure and names, added test for vtk{point/voxel}cloud
2015-10-09 11:24:26 +00:00
1bd8167445
requires core module and is most likely not used.
...
When needed, a Complete, lean redesign is simpler than updating to current coding style
2015-10-06 18:11:58 +00:00
22048cb546
fixed a bug
2015-10-02 01:59:59 +00:00
863fe5ddf0
needs modules “math” and “random” for user-supplied conditions…
...
(do not remove through pyflakes—shall we introduce dummy code to keep the modules “active”?)
2015-09-29 22:27:07 +00:00
202ee00049
Eliminated redundant searches for similar orientations in neighboring points…speeds up script by 2 orders of magnitude
2015-09-28 19:03:24 +00:00
55dc2b419a
warn if unexpected file size is encoutered
2015-09-24 17:07:27 +00:00
f4d4a8e1ec
adopted philips changes for reporting, using pyflakes to clean up
2015-09-24 09:24:42 +00:00
3c901e5549
added option for Euler angle output in degrees
2015-09-23 23:05:28 +00:00
fb48719283
fixed critical bugs
2015-09-15 19:02:59 +00:00
6f20651250
copy and paste error and new interface for test
2015-09-12 19:29:34 +00:00
6683c1fb73
fixed a bug
2015-09-12 16:34:31 +00:00
5f9fae1b75
simplified reporting using "emph"
2015-09-11 12:55:43 +00:00
e0d5cef047
Script to merge multiple ASCIItables. Stops at end of shortest one.
2015-09-09 22:22:29 +00:00
70f906a2c4
follow new syntax and bugfix, marc 2014 is default
2015-09-09 16:45:49 +00:00
c9dcb41bac
fixed sorting logic to respect numerical values of vector data (i.e. 1,2,3,….,10,11,… instead of 10,11,12,1,2,…)
2015-09-08 23:55:44 +00:00
c2d27d56fa
updated to new ASCII table style
2015-09-08 15:26:40 +00:00
9a2c49ff50
corrected label header
2015-09-08 13:45:46 +00:00
cf90b764f8
calculation was for nyquist freq not fully correct.
...
See Notes on FFT-based differentiation
Steven G. Johnson, MIT Applied Mathematics
Created April, 2011, updated May 4, 2011:
2015-09-05 11:51:36 +00:00
08f8746182
made some more scripts working again
2015-08-31 21:22:44 +00:00
8ff79e1eb0
NaN now considered transparent
2015-08-31 17:41:00 +00:00
8f79744f2c
now works with (rounded) floating point numbers as mapping indices
2015-08-31 16:01:11 +00:00
6100185855
switch to new ASCII table class was buggy, using damask.util.emph
2015-08-31 11:00:45 +00:00
115518a2c8
minor changes in commit and setting the script ID properly
2015-08-29 15:10:43 +00:00
cff6307779
Update existing value(s) to expression(s) respecting condition.
2015-08-29 00:54:45 +00:00
d8afe9be23
Add scalars, vectors, and/or an RGB tuple from an ASCIItable to existing VTK rectilinear grid (.vtr/.vtk).
2015-08-25 00:39:37 +00:00
cec6d7d220
for generating rectilinear grid of either cell type or point type from ASCII table.
2015-08-24 20:48:50 +00:00
7961b486cb
now compatible with updated Orientation.disorientation() output, i.e., select item [0] (the quaternion).
2015-08-24 14:20:09 +00:00
c215139ce1
now works with recent changes of ASCIItable and with STDIN to STDOUT.
2015-08-24 14:01:24 +00:00
afc88c7029
now works with recent changes of ASCIItable.
2015-08-24 13:42:29 +00:00
38992fdc37
now use outsourced damask.util methods
2015-08-23 23:19:40 +00:00
63d5506388
adopting further simplifications provided through ASCIItable class.
2015-08-20 19:42:05 +00:00
9439cf7278
add cumulative (first to current) values of given labels to table
2015-08-20 19:40:45 +00:00
2a13d78196
did not run
2015-08-18 17:24:15 +00:00
70daa8663f
adoption of new ASCIItable API
2015-08-18 14:37:32 +00:00
ca1fe6bb82
updated to new ASCII table style
2015-08-18 07:56:03 +00:00
d0b75b5a10
fixed table.croak error in last commit
2015-08-18 04:41:36 +00:00
befd6aa7ff
fixed stderr output (croaking..) as per new ASCII table style
2015-08-18 04:33:45 +00:00
ac7f443595
adopted new ASCIItable API
2015-08-13 21:25:08 +00:00
7ca1e77495
bug fixing
2015-08-13 08:32:09 +00:00
3e65c324de
adopted changes in ASCIItable API
2015-08-12 21:52:33 +00:00
1149053c61
updated to new ASCII table style
2015-08-12 20:59:10 +00:00
35863e0229
fixed averageDown and made it's test running
2015-08-12 13:43:05 +00:00
bceeb0964c
corrected calculation of expected file size for legacy files beyond the 4 GB limit
2015-08-10 18:48:48 +00:00
126cea24ce
fixed syntax and undefined variable calling errors
2015-08-09 22:12:49 +00:00
a4772343b0
adopted new ASCIItable API. some polishing.
2015-08-07 22:08:54 +00:00
d4e748b654
outsourced multiple repetitive functions into ASCIItable class.
...
changed ASCIItable API from file-handles to filenames.
adopted these changes in pre and post processing scripts.
unified behavior and look.
fixed bugs here and there.
improved functionality.
2015-08-07 19:03:26 +00:00
020a3e2634
superfluous since same can be (even more flexibly) accomplished with:
...
reLabel -l old -s old+tag
2015-07-26 00:41:42 +00:00
0db33f21b5
superfluous since same can be accomplished with:
...
showTable -l -d (labels and data)
2015-07-26 00:39:32 +00:00
657ed7ed35
group voxels/pts by orientation and position, require spicy.
2015-07-24 13:30:33 +00:00
e08b7bd02e
forgot to rescale transparency mask by pixelsizes.
2015-07-16 22:34:26 +00:00
3c9d6df889
fixed typo in last commit
2015-07-15 18:15:39 +00:00
6ebc490207
fixed broken functionality by adopting new ASCIItable class output for data_readArray().
2015-07-15 16:57:03 +00:00
dce0501358
script to rename labels in an ASCIItable
2015-07-10 16:28:01 +00:00
f8658ffea1
added “gap” value to render pieces of resulting image transparent.
2015-07-07 14:53:55 +00:00
812d17f91c
streamlined column processing based on recently introduced asciitable functionality.
2015-07-01 15:48:34 +00:00
ef243d3e19
added references
2015-06-30 14:52:48 +00:00
47249bb52a
added possibility to scale deformation fluctuation field.
2015-06-29 09:44:49 +00:00
9b1f16e99e
report data range.
...
gracefully deal with constant field (below 1e-8 noise).
2015-06-19 11:36:21 +00:00
94423cc7ac
added scriptID line “ removed during last commit”
2015-06-17 19:47:50 +00:00
012c830eff
removed writing of debugging statement to final output
2015-06-17 19:44:01 +00:00
e440305532
streamlined ASCIItable error checking.
2015-06-17 06:52:43 +00:00
5cc7b60a88
simplified processing of ASCIItables by utilizing the improved class methods.
...
modernized file looping.
2015-06-16 17:21:24 +00:00
c089ff9256
now with $ID$ and correct line endings…
2015-06-15 18:13:06 +00:00
6086baba52
Generate PNG image from scalar data on grid deformed by (periodic) deformation gradient.
2015-06-15 18:12:38 +00:00
37792f67df
automatically figure dimension of labels to tag.
2015-06-13 11:55:20 +00:00
e243632eb5
simplifications by adopting functionality provided by new asciitable class methods.
2015-06-08 05:07:14 +00:00
d99e34d870
typo caused problems with more than one tensor
2015-06-06 15:42:29 +00:00
129446e687
simplified script. deals now only with single format at a time. result is printed to STDOUT unless “basename” option specified.
2015-06-06 11:12:07 +00:00
bb9e080790
input file handling now save for large file count.
...
reshape input rotation matrix to (3,3).
2015-06-05 11:47:27 +00:00
5adbe74b10
changed library function name table.labels_index() to table.label_index()
2015-06-05 11:44:17 +00:00
2877066a6c
removed debug statement and simplified
2015-06-04 08:51:10 +00:00
bb677a26aa
added interface for predefined colormaps
2015-05-29 18:50:54 +00:00
92654dc2cd
fixed syntax bug, instantiating of Color object, and file closure.
2015-05-29 18:36:09 +00:00
54746c85d3
fixed bug for only blacklisting.
2015-05-28 22:31:32 +00:00
c327735c0d
order of whitelist is maintained in output (only if no blacklist is specified). allows to rearrange column order in tables.
2015-05-27 23:02:11 +00:00
4107d5d1d2
Script to calculate Quaternion from input orientation matrix
2015-05-26 06:38:48 +00:00
5900fa4bf5
corrected defaults and simplified loops
2015-05-25 10:49:20 +00:00
1f160dfd72
FFT was at single precision only
2015-05-24 16:35:37 +00:00
e8fb49edc6
missing bracket
2015-05-22 06:17:35 +00:00
737e474cea
consistent handling of random number per file and always reporting as comment, fix for permuteData needed because of new asciitable behavior
2015-05-22 05:56:49 +00:00
fbfa55e910
adjusted to new table style and naming of output
2015-05-22 04:57:05 +00:00
f363d81de5
simplified column parsing
2015-05-21 21:54:47 +00:00
2349e6c79c
standard way of reporting
2015-05-21 16:04:19 +00:00
14b921f6d5
corrected help text.
2015-05-21 00:13:50 +00:00
df5dd98576
simplified boolean dictionaries to “if else” constructs.
2015-05-21 00:13:11 +00:00
acc2cb656b
simplifications due to better functionality available through asciitable.py
...
output filename format has slightly changed: binned-X-Y_weighted-W_
2015-05-21 00:08:32 +00:00
439d778cc0
simplified column check.
...
fixed typos and improved help.
2015-05-20 23:21:35 +00:00
973f092fd9
similar to imageData but uses RGB triplet as color value instead of mapping a scalar.
...
Can only use columnar data and not 2D arrays, though.
2015-05-19 21:15:15 +00:00
ee65b269ad
simplified data column determination.
2015-05-19 21:14:19 +00:00
f7faa3eeca
finally fixed the bug in the transformation and incorporated rotation to conform to TSL convention
2015-05-18 22:28:24 +00:00
03fef5fd6e
simplified option parsing
2015-05-15 13:49:16 +00:00
6a38b4396f
simplified help
2015-05-15 13:34:52 +00:00
a3bed5cc42
short options conflicting with typical use
2015-05-15 10:33:32 +00:00
a451a69c2c
corrected default type (only list for 'extend')
2015-05-14 18:48:15 +00:00
3e8f16c515
range parameter is now autoscaled to account for -log option, i.e. range is always given as bounds of original data
2015-05-13 13:45:26 +00:00
b0a37497a1
fixed buggy coordinate transform.
2015-05-12 15:30:00 +00:00
6a98c7efad
simplified option parsing
2015-05-11 20:12:31 +00:00
2102fadfc7
improved help for automatic documentation
2015-05-11 19:47:52 +00:00
537c42d146
script to transform coordinate system at APS beam line 34-ID-E from X,Y,Z,F to strain x,y,z
2015-05-11 14:15:50 +00:00
eff71b418b
now working with corrected asciitable
2015-05-10 20:59:23 +00:00
b60f868a76
renumbering asciitable when readArray for selected columns only
...
test no longer for deleteColumn
2015-05-10 11:29:11 +00:00
8bf7a7ef6a
some beautifications
2015-05-10 10:58:32 +00:00
c0a9141c8f
updated help to enable automated documentation
2015-05-10 10:56:02 +00:00
a03b1ede99
improved help for automatic documentation
2015-05-10 08:59:21 +00:00
d87b70fe49
filterTable can do the job
2015-05-09 21:33:17 +00:00
18831e0e80
improved help for automatic documentation and simplified some scripts
2015-05-09 21:32:23 +00:00
47b8605733
improved help for automatic documentation and simplified some scripts
2015-05-09 13:01:31 +00:00
59e546e3d7
improved help for automatic documentation and simplified some scripts
2015-05-09 12:45:30 +00:00
cb42fb9c5d
clarified help text.
2015-05-05 16:58:56 +00:00
58b3d017bd
changed option name from “invertColor” to “invert”
2015-05-01 17:58:10 +00:00
c05df20370
throw error message when DAMASK output obviously not present in T16 file
2015-04-28 17:54:00 +00:00
895421e677
changed from core module fftw to fftwpack from latex, tolerances need to be less strict
2015-04-24 08:07:13 +00:00
790aa32b1b
fixed string to character splitting of weight column label
2015-04-13 20:24:03 +00:00
4bcc80911e
changed grid to float from (wrong) integer type.
...
row and column probability density normalization now takes place BEFORE limiting data range.
2015-04-13 19:55:28 +00:00
5257a2161f
added options for x and y normalization
2015-04-09 06:45:21 +00:00
57a2c90d30
corrected according to vtk specification and remove an unused option
2015-04-08 18:48:35 +00:00
0544706c7b
corrected help for legacy format
2015-04-08 12:51:40 +00:00
92a67e1a9d
geom_fromAng.py crashed when found empty line (eg. at the end of the file), now fixed
2015-04-01 14:42:25 +00:00
a1956436be
fixed bug introduced last time when searching for keywords in spectralOut header
...
made reading in of header more robust by explicitly using the information given by fortran specifies the data length
introduced a legacy mode again, now it is used to read old spectralOut files prior to rev 4017
2015-04-01 10:02:21 +00:00
38943c1e94
improved help
2015-03-29 15:37:40 +00:00
913c5347a5
removed handling for old legacy format (we might introduce a new one)
2015-03-29 09:08:42 +00:00
66d4ff097f
removed obsolete comment
2015-03-28 11:44:17 +00:00
8a30021202
cleaned up core modul
2015-03-27 14:10:18 +00:00
1ee81e74ea
more patches to get the tests running again:
...
- fixed increment counting in postResults to current output scheme
- corrected node coordinates calculation
- some work on restart (restart test still not running)
2015-03-26 21:19:28 +00:00
fe4373a9f9
updated post processing script for MPI IO spectralOut file
2015-03-25 16:09:56 +00:00
1a3bfc7d1f
updated according to new convention for ip and nodes
2015-03-24 13:52:40 +00:00
12cb5e56fe
fixed interpretation 'spectralOut' header. Seem to have been buggy all the time, but manifested itself only after keyword change. Also added ':' after keywords to be more robust
2015-03-15 15:29:38 +00:00
df2ee87a7c
corrected help
2015-03-13 14:47:22 +00:00
c4f639dbfb
prevent crash in option parsing
2015-03-13 14:46:40 +00:00
def6d6b878
re-introduced determination of elem column
2015-03-12 06:20:40 +00:00
3f340ffac9
fixed bug for table data without labels in header
2015-03-11 20:39:14 +00:00
72efc7b30c
renamed resolution -> grid, dimension -> size
2015-03-11 08:55:48 +00:00
0dde6539ed
renamed from 1_ip to 1_ipinitialcoord
2015-03-11 07:22:11 +00:00
eb1561b528
changed postprocessing to use 1_ip instead of ip.x etc, plus corrected test files headers
2015-03-10 21:15:05 +00:00
271c9eed8b
use 1_ip instead of ip.x
...
Old format still as fallback option to support legacy files
2015-03-09 12:52:43 +00:00
4d587b1bf9
introduced 'alias' for ip.x by first searching for 1_ip
2015-03-09 11:32:16 +00:00
639b030c65
shortened code for opening input file list
2015-03-06 17:04:44 +00:00
654aacf207
removed invalid options (options.packing, options.shift)
2015-03-05 21:41:53 +00:00
53b40662ec
now with executable, correct line endings, and ID tags.
2015-02-11 17:26:56 +00:00
d5f9f543ca
Script to generate PNG image from given column (or 2D data in overall ASCIItable) with custom colormap and pixel sizes.
...
Supersedes “imageFromData” from “Code” repository.
2015-02-11 17:25:49 +00:00
9eae665365
fixed ‘too many files open’ issue when processing a large list of input tables.
2015-02-11 17:22:47 +00:00
1b1ed3bbcf
removed unnecessary lines
2015-02-11 06:18:08 +00:00
63434c2ddb
corrected error checking for correct type
2015-02-09 08:57:14 +00:00
7edd209ce4
corrected wrong name in add..., more verbose error checking for geom_from...
2015-02-07 22:22:28 +00:00
6140285ddd
small changes (use ip.x instead of 1_ip). Probably we should modify postResults to use the 1_, 2_, 3_, standard notation for ip as well
2015-02-07 18:13:51 +00:00
e4a94aa72b
put changes on algorithm from geom_fromEuclideanDistance into addEuclideanDistance
2015-02-07 17:11:46 +00:00
2c9c04eb76
added script to replace all rows of an ASCII table by a single row containing their average
2015-01-23 00:57:10 +00:00
5be9a75cff
fixed indentation
2015-01-22 09:04:01 +00:00
c08f704dee
added Id + a little help
2015-01-07 19:29:27 +00:00
ca58216134
added missing math module import
2015-01-05 12:25:03 +00:00
3e3c13bf0b
added missing math module import
2015-01-04 21:02:17 +00:00
5e8fff13d9
worked on the vtk binary out, still some problems with multicomponent datatypes
2014-12-18 21:46:38 +00:00
6604d0f8e8
polishing
2014-12-18 19:26:52 +00:00
89f8ba979e
Add x,y coordinates of stereographic projection of given direction (pole) in crystal frame.
2014-12-13 00:12:55 +00:00
b17dcd7652
added options ’—origin’ and ‘—geom’. Latter interprets the geom-header to derive voxel sizes.
2014-11-18 15:26:59 +00:00
461a3fa979
fixed syntax error and added ‘—render’ option to immediately see output on screen
2014-11-18 15:24:09 +00:00
a3196669ea
exchanged deprecated data array read function
2014-11-18 15:22:00 +00:00
7136db1fd8
fixed syntax error: ’options.error’ —> ‘parser.error’ for error handling
2014-11-18 15:20:57 +00:00
99ffa554eb
added ‘1_*’ to ‘*’ as possible column label indicator
2014-11-18 15:20:10 +00:00
b5ef329f34
changed default position column format from .x,.y,.z to more standard 1_,2_,3_
2014-11-18 15:18:27 +00:00
f6741138e7
had badly messed up the file handling in commit 3630. STDIN did not work, files were not checked for existence…
2014-10-29 13:27:40 +00:00
bdd2d55383
small bug fix for last commit
2014-10-24 06:36:01 +00:00
13ba71a314
fixed bug where option.condition was altered in processing of first file, thus preventing additional files from seeing the same user input.
...
changed file handle setup to allow for large lists of input files.
2014-10-23 21:23:10 +00:00
Philip Eisenlohr