Commit Graph

417 Commits

Author SHA1 Message Date
Philip Eisenlohr 0c1657693f dirty (but working) fix to adopt table.labels now being table.tags: table.labels --> table.labels(raw = True) 2016-05-17 10:52:21 -04:00
Philip Eisenlohr 9103ee544b Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development 2016-05-17 09:52:18 -04:00
Aritra Chakraborty 8d6c601a45 fixed python flake complaints. 2016-05-16 20:17:17 -04:00
Aritra Chakraborty 1c36380a8a fixed typo... 2016-05-16 20:05:57 -04:00
Aritra Chakraborty dc6260be58 changed "labels" property to "tags". added method to inquire about (abstract) labels, i.e. interpreting the tag list to distill underlying label "meaning". 2016-05-16 19:54:00 -04:00
Philip Eisenlohr 280076e7ef removed (probably obsolete) warning about missing h5py module. 2016-05-11 10:04:01 -04:00
Martin Diehl d3ee2c05b9 =removed remaining IDs 2016-05-11 11:43:21 +02:00
Martin Diehl 7f24fe15ed removed svn ID from python files 2016-05-11 11:37:59 +02:00
Martin Diehl a21e8cd863 usind explicitly python2 to run in environments with python 3 as default 2016-05-11 11:01:39 +02:00
Philip Eisenlohr 5d4d78b079 expanded functionality to treat (white space-containing) strings and empty ("") data. 2016-04-28 23:11:06 -04:00
Martin Diehl 7ce208019c Merge branch 'development' into miscImprovements 2016-04-25 12:36:02 +02:00
Philip Eisenlohr ea24becdd4 added "report_geom" shortcut to croak geometry info 2016-04-24 11:20:55 -05:00
Philip Eisenlohr 45e237058b fixed malfunctioning table.label_indexrange(listOfLabels). can now be used as numpy slice. 2016-04-24 10:07:37 -05:00
Philip Eisenlohr 54dec3ea2a remove CR and LF from labels and info lines. Can happen if multiline shell input is parsed... 2016-04-20 15:46:39 -04:00
Martin Diehl 72639d174b fortran code was translated by philip 2016-04-15 00:25:12 +02:00
Martin Diehl 0632dc1308 pyflakes complained 2016-04-15 00:22:41 +02:00
Martin Diehl 573d10f1e1 Merge branch 'development' into NoCoreModule 2016-04-15 00:05:38 +02:00
Martin Diehl 82063494fd adopted to new json format of paraview
introduced "standard" colormaps for stress, strain, and orientation
file is now implicit the first argument without key (in line with other scripts)
2016-04-11 19:47:07 +02:00
Philip Eisenlohr da29b1a361 removed line continuation characters (not needed within parentheses) 2016-04-05 13:29:36 -04:00
Philip Eisenlohr 73640587d5 fixed buggy query-by-label-index 2016-03-27 16:26:51 -04:00
Martin Diehl 3824b683bc removed extra cython file, symlink to standard orientation instead 2016-03-24 15:06:04 +01:00
Martin Diehl c73382e51f further cleaning 2016-03-24 14:36:24 +01:00
Martin Diehl d765282165 save fortran code 2016-03-24 14:20:18 +01:00
Martin Diehl 143a868dad files resulting from compilation should not be part of the repository 2016-03-23 11:05:00 +01:00
Martin Diehl fafedd5cd6 Merge branch 'LargeFiles' into development 2016-03-22 15:45:42 +01:00
Philip Eisenlohr 1b22b6e4ee replaced variable interpolation into strings by "%" with .format() method 2016-03-21 10:26:30 -04:00
Philip Eisenlohr 8cd1f027b3 bug fixing. 2016-03-21 08:51:56 -04:00
Philip Eisenlohr 01a5343ca2 added another backgroundMessage animation. generally cleaned code a slight bit. 2016-03-20 20:58:10 -04:00
Philip Eisenlohr a41cd3df40 added "strict" option to reading microstructure from geom file. will now complain if data mismatches with grid. 2016-03-20 16:46:35 -04:00
Zhuowen Zhao d42f8d5fd4 added possibility to read real numbers as microstructure indices (not only integers) 2016-03-17 17:42:05 -04:00
Martin Diehl 7a4e9856c5 Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development 2016-03-14 18:47:54 +01:00
Martin Diehl fdd4ab483e core.so is not part of the repo 2016-03-14 05:51:52 +01:00
Martin Diehl 2dbdf9a72f all symbols need to be representable in unicode 2016-03-13 18:21:25 +01:00
Martin Diehl efde4d363d changed encoding 2016-03-07 09:56:14 +01:00
Martin Diehl a4bbdd5ecb further commenting, removing not used variables and code (marc2vtk) 2016-03-04 19:06:36 +01:00
Martin Diehl d1e8f69857 added docstrings etc 2016-03-04 17:55:11 +01:00
Martin Diehl 24391b5398 checked with prospector, adopted mainly docstrings 2016-03-04 17:53:55 +01:00
Martin Diehl 9a405ef41b using more stable way of handling unicode printing, cleaning unicode delete from output of execute 2016-03-04 17:23:38 +01:00
Martin Diehl 75480bc677 modified background threading because using it in postResults led to an dead lock.
rest modifications are just style
2016-03-04 15:22:01 +01:00
Martin Diehl 4d8aad36f1 first round of libraries 2016-03-01 23:02:47 +01:00
Martin Diehl 2a3e42a906 prevent import errors (e.g. when using Abaqus, having it's own python without scipy) 2016-02-02 23:24:44 +01:00
Martin Diehl 4fa2a58a19 needed to adopt to new test env (not perfect yet, but keeps things going) 2016-01-29 19:21:04 +01:00
Martin Diehl f2c7eea161 git compatible way of version handling for Fortran and Python 2016-01-27 16:48:27 +00:00
Martin Diehl 81a8b2c4ed color lib for output 2016-01-05 18:17:55 +00:00
Martin Diehl 120b2b8bd2 added test for hybridIA 2015-12-22 22:17:15 +00:00
Martin Diehl 0cfe35dfe6 consistently removing leading and trailing whitespace 2015-12-22 15:59:01 +00:00
Martin Diehl bbb00b30e8 using numpy random 2015-12-17 21:26:59 +00:00
Martin Diehl 37aa559bd4 fixed missing structure type in material.config, small changes in the other code 2015-12-15 14:30:17 +00:00
Martin Diehl 97b96f13b2 updated installation for testing 2015-12-14 21:31:47 +00:00
Martin Diehl 1f08d0fbf6 verbose option for compareTables, new option to filter (now before and after normalizing) 2015-12-11 17:23:36 +00:00
Martin Diehl c3dc05c53a continued work on test class and adopted some tests 2015-12-04 22:40:39 +00:00
Philip Eisenlohr a18a1066e2 started to rework test class. Martin probably needs to check and continue improving on this. 2015-12-03 21:52:03 +00:00
Philip Eisenlohr fc2d79e17b added more animations… 2015-12-02 23:08:18 +00:00
Martin Diehl 0e76ef85c1 checking return code in util.exececute, cleaning makefile, deleted dummy docs 2015-12-02 13:21:17 +00:00
Martin Diehl 0ffcb7fdaf cleaning 2015-12-01 16:37:20 +00:00
Martin Diehl 161e637ba6 not needed any more (at more usefull position in damask.util) 2015-11-30 16:30:35 +00:00
Philip Eisenlohr 38c536b6b7 improved unicode handling.
background message is now stoppable.
background message not “jumping” (multiplying) anymore.
2015-11-20 16:15:34 +00:00
Philip Eisenlohr 30a481f152 fixed forgotten symmetry property for average orientation. 2015-11-14 04:36:46 +00:00
Philip Eisenlohr 2b5cb08c4d new method “head_putGeom” translates info-array into geom-description 2015-11-14 01:48:16 +00:00
Philip Eisenlohr 6211a9faad symQuats-related functions can take optional argument to downselect return values.
“getAverageOrientations” —> “average” and takes optional multiplicities of orientations in list.
2015-11-14 01:46:44 +00:00
Martin Diehl b700721905 comment on literature 2015-11-08 11:44:46 +00:00
Philip Eisenlohr 519484233c can now deal with “empty” header line.
example:
# some comment
# further stuff
1_dim 2_dim
34 33
1 22

would work with “labeled”=True and stores the first two lines as “info”.
2015-11-03 21:14:45 +00:00
Martin Diehl 4ac9ef602e still trying to find a stable solution on all machines 2015-10-29 21:51:57 +00:00
Aritra Chakraborty 9ea0898cd9 corrected the convention added yesterday; “proper” and ‘improper” was the wrong way around. “proper = True ” considers the bigger (2 adjacent) SST. In general, an improper rotation is implicitly assumed when projecting a pole into the (single) SST, hence this is termed “improper” now. 2015-10-23 20:16:01 +00:00
Philip Eisenlohr 15963391aa inSST and inversePole now can consider the secondary SST related to improper rotations. Secondary SST is immediately neighboring (positively rotated around Z). 2015-10-22 21:15:15 +00:00
Martin Diehl 31579b3f88 tolerances caused problems, introduced new funtionality based on np.allclose 2015-10-22 05:59:11 +00:00
Franz Roters b676ed0085 support for Marc 2010 was dropped a long time ago 2015-10-20 13:32:48 +00:00
Franz Roters a087eedd54 added support for Marc2014.2 (so far installed on maws14 only) 2015-10-20 13:25:59 +00:00
Martin Diehl e72ae63873 geom canvas crashed for some parameters, now giving error message. table class now handles dismiss correctly 2015-10-14 21:35:56 +00:00
Philip Eisenlohr 7df8d95cd0 slightly cleaner way of dealing with disorientation calculation when axis not required to fall into SST. 2015-10-09 13:03:10 +00:00
Philip Eisenlohr 26f8f74310 undone np.unique of columns since this would introduce the unwanted side-effect of (messily) sorting columns. user expects to get sorting as provided through command line. 2015-10-09 12:55:30 +00:00
Martin Diehl 4c46d155ec line continuation not needed 2015-10-09 10:24:17 +00:00
Martin Diehl 61090c955d removed code doubling 2015-10-09 05:51:58 +00:00
Martin Diehl 851d2e1b2c prevent to load columns more than once\n @Philip: OK? 2015-10-08 17:47:00 +00:00
Philip Eisenlohr 3b0dc374bb now using ‘emph’ in reporting function instead of code doubling. 2015-10-07 01:07:56 +00:00
Philip Eisenlohr 801d57af4c fixed buggy behavior caused by assigning string instead of single-item list to readBuffer. 2015-10-07 01:03:26 +00:00
Martin Diehl 6e05082133 might be needed in multicore env 2015-10-06 18:01:31 +00:00
Martin Diehl 95a8b54996 buggy behavior when read buffer contained string (len > 0, but no pop() method)
@Philip: please check if intended behavior
2015-10-06 16:19:37 +00:00
Philip Eisenlohr e089e60202 transparently deal with one-dimensional array output 2015-09-30 18:44:54 +00:00
Philip Eisenlohr b2243ae3c1 small polishing 2015-09-29 22:25:57 +00:00
Martin Diehl 948aa0c544 was missing in last commit 2015-09-24 10:01:15 +00:00
Philip Eisenlohr 2aa1073949 relocated “croak” and “report” functionality to here. needs to be altered in all scripts that still use the ASCIItable class for those… 2015-09-22 21:00:18 +00:00
Martin Diehl 6a3a0f3859 allow asciitable to use file handle instead of string (following e.g. numpy.genfromtxt) 2015-09-16 19:44:11 +00:00
Harsha Phukan 24bd3a6eee added “non-strict” version to find disorientation, neglecting the search for axis falling into SST (has linear instead of quadratic effort). 2015-09-16 17:07:02 +00:00
Harsha Phukan 8a05584924 bg.message does not require symbol selection anymore—will pick random if nothing specified… 2015-09-15 19:02:00 +00:00
Martin Diehl 5f9fae1b75 simplified reporting using "emph" 2015-09-11 12:55:43 +00:00
Philip Eisenlohr 31bb27268c removed dangerous property overload (.asQuaternion() —> .quaternion) 2015-09-09 22:37:18 +00:00
Tias Maiti 7495b33b68 label_dimension dropped indices >9 due to buggy string comparison… 2015-09-08 23:12:45 +00:00
Chen Zhang ba418a5c97 reflect recent changes in orientation class 2015-09-03 16:50:49 +00:00
Tias Maiti eb5ad7528f fixed bug in asEulers() output in degrees 2015-08-29 23:22:32 +00:00
Martin Diehl 6848d83d13 behavior of IO_stringPos was unsafe in some situations, also took the chance to rename the variables used in its context to a more meaningful name.
functions in the core module are not used, including kdTree
2015-08-28 07:38:48 +00:00
Chen Zhang f4145dd505 add numpy header location in the setup script. 2015-08-25 18:06:36 +00:00
Philip Eisenlohr 636eb8a087 multiple fixes and improvements.
1) asAngleAxis got “degrees” switch, fixed buggy output for negative angles, now angles are always non-negative.
2) removed rotateBys.
3) asEulers corrected for cases w==z or x==y.
4) added method symmetryQuats.
5) calculation of disorientation (finally) fixed, returns tuple (disorientation quaternion, index symA, index symB, boolean whether A—>B or B—>A).
2015-08-24 13:39:09 +00:00
Philip Eisenlohr 858fe7e897 prevent closing sys.stdin or sys.stdout 2015-08-24 00:40:52 +00:00
Philip Eisenlohr 7ceb7f7614 fixed problem when reading single label through data_readArray 2015-08-23 23:18:34 +00:00
Philip Eisenlohr 681b7f0831 added ‘emph’ method.
additional background message animations.
2015-08-22 17:02:49 +00:00
Philip Eisenlohr 6ba76c3832 introduced public line object holding currently read data line as string.
label_append now has option to overwrite (reset=True) labels that were read originally.
data_writeArray maintains full significant digit representation as default.
2015-08-20 19:38:06 +00:00
Martin Diehl 22c52fbd32 cleaned core module 2015-08-12 18:48:09 +00:00
Philip Eisenlohr 93dd9f5c09 bug fix regarding self.tmpext.
added check for access rights when overwriting original file.
2015-08-12 18:41:44 +00:00
Martin Diehl a29240242b standard name for numpy is np 2015-08-12 18:32:28 +00:00
Philip Eisenlohr 64515d7aca simplified interface:
name == None: read from stdin
outname == None and not readonly mode: do in-place substitution of name (with transparent file renaming upon table.close)
2015-08-12 17:42:38 +00:00
Martin Diehl f9348398ce removed old file, added possibility to normalise euler angels to standard range, added svn properties 2015-08-12 15:15:33 +00:00
Martin Diehl 35863e0229 fixed averageDown and made it's test running 2015-08-12 13:43:05 +00:00
Martin Diehl 36caddcc24 adjusted to new ASCII table file handling 2015-08-12 12:51:47 +00:00
Chen Zhang 3991813595 fix syntax error regarding several static method 2015-08-10 21:08:00 +00:00
Philip Eisenlohr 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
Chen Zhang dfe0991134 adding property alias for Orientation class to simplify syntax. 2015-08-04 20:38:06 +00:00
Chen Zhang 1ec3639cf1 use pure python implementation of orientation class as default 2015-08-02 17:49:38 +00:00
Chen Zhang fbb7f9b11b remove deprecated function from math.f90 2015-07-29 20:49:42 +00:00
Chen Zhang 9287d6f15f make the interface for Symmetry class compatible with pure python version. 2015-07-29 19:39:30 +00:00
Chen Zhang 5f74f3e95e add Cython version of orientation module to provide faster orientation calculation. 2015-07-29 19:23:06 +00:00
Chen Zhang 70606770d0 correct two typos in Quaternion class 2015-07-28 20:10:27 +00:00
Chen Zhang bfedf037c6 add asAngleAxis() to Orientation class 2015-07-22 21:49:24 +00:00
Chen Zhang 08f4495721 changed readArray default behavior to reading always scalars when columns are referenced by number 2015-07-21 20:44:40 +00:00
Philip Eisenlohr c46e639a38 fixed bug preventing first line to be read when using readArray without labels. 2015-07-09 03:40:15 +00:00
Yannick Naunheim 5fe65bfcc3 corrected OR models and set up simple test to check them 2015-06-29 16:02:56 +00:00
Martin Diehl 50bcfe6e0d possibility to give fixed seed to random orientation 2015-06-26 06:32:25 +00:00
Martin Diehl 6aaf074651 bug fix 2015-06-25 16:16:01 +00:00
Martin Diehl f10dfa311a fixed ORs 2015-06-25 12:00:08 +00:00
Philip Eisenlohr 2d8af638b0 added optional keyword `degrees´ to q.asEulers().
added methods inFZ, equivalentQuaternions, and equivalentOrientations to Orientation class.
general polishing…
2015-06-21 12:05:17 +00:00
Philip Eisenlohr 16edd1693d now only trying to close input and output tables.
corrected buggy behavior in case no columns found in data_readArray.
2015-06-19 06:08:09 +00:00
Philip Eisenlohr 83547ce29f condensed multiple import statements into general one at module start. 2015-06-15 15:36:58 +00:00
Philip Eisenlohr 66ce1d0b33 speed up for inversePole method. Now only performing symmetry equivalence when asked for SST. 2015-06-13 11:51:10 +00:00
Philip Eisenlohr 0efbd4b11f added Colormap.color(fraction) function to interpolate a color from the colormap.
cleaned Colormap.export by now relying on new interpolation function.
2015-06-13 11:46:32 +00:00
Philip Eisenlohr 3d7dfba40a syntax polishing 2015-06-13 11:43:34 +00:00
Martin Diehl d894900c2e added support for marc 2014:X 2015-06-11 18:19:52 +00:00
Philip Eisenlohr 48f31f13a6 label_index now transparently searches for “1_”+label if label itself not found.
added label_dimension method returning the dimension of the requested object, i.e. 1, 3, or 9 as typical outcomes.
2015-06-08 05:02:11 +00:00
Philip Eisenlohr 83d5686995 added check before trying to delete/dismiss file 2015-06-06 11:18:39 +00:00
Philip Eisenlohr a8d61a29d6 added newlines at end of colormap.exports 2015-06-06 11:09:15 +00:00
Philip Eisenlohr 5adbe74b10 changed library function name table.labels_index() to table.label_index() 2015-06-05 11:44:17 +00:00
Tias Maiti 9d5ca8b631 orientation matrix shape checked in “ fromMatrix “ function 2015-05-28 21:52:05 +00:00
Philip Eisenlohr 58eb4fc301 transparent (3,3) reshape of matrix when generating orientation. 2015-05-27 18:56:18 +00:00
Harsha Phukan c8d774f456 adopted math from Martin Baker to calculate quaternion from matrix representation. 2015-05-22 20:04:05 +00:00
Philip Eisenlohr 4bd44f8e43 better robustness against scalar arguments and “None”. 2015-05-21 21:53:54 +00:00
Philip Eisenlohr 99adf42f0f improved robustness of labels_index determination.
fixed errors in data_readArray and improved functionality. Can now cope with list of columns. reads all valid columns returning list of invalid ones. updates table.labels accordingly.
2015-05-21 00:02:32 +00:00
Philip Eisenlohr 06f017effa added possibility to dismiss (delete) output file upon closing an ASCIItable.
“None” labels are disregarded in labels_index() method.
2015-05-19 21:11:49 +00:00
Philip Eisenlohr 9f569d04c6 added “.close()” method to close input and output at the same time.
accept header only if space present between number and “head” string.
2015-05-19 20:35:56 +00:00
Martin Diehl 5d19e55eb4 corrected access by number 2015-05-15 13:35:50 +00:00
Martin Diehl b30eba3919 introduced (untested) OR calculation 2015-05-15 12:44:48 +00:00
Martin Diehl fa1368204d fixed bug in asciitable when updating labels for readArray, fixed checking for euler angels presence in tessellation, improved help 2015-05-14 17:07:50 +00:00
Martin Diehl b60f868a76 renumbering asciitable when readArray for selected columns only
test no longer for deleteColumn
2015-05-10 11:29:11 +00:00
Yannick Naunheim 88e16f9344 corrected Bain model 2015-05-08 14:45:59 +00:00
Yannick Naunheim 90ae536204 introduction of orientation-relationship (OR) models: Kurdjumov-Sachs (KS), Nishiyama and Wassermann (NW), Greninger-Troiano(GT), Bain 2015-05-08 14:14:44 +00:00
Martin Diehl 4448187c1e functions have been removed in previous commit 2015-05-05 14:44:31 +00:00
Martin Diehl 9694d63874 introduced option mute output to screen 2015-04-22 18:47:45 +00:00
Chen Zhang 43b665ba48 add getAverageOrientation() to Orientation class as class method. 2015-04-02 19:15:09 +00:00
Martin Diehl 32f9e7f9d8 now giving just a 'Remark' when h5py is not found 2015-04-01 14:43:34 +00:00
Tias Maiti f5801601d8 fixed UnboundLocalError (calling variable before assignment) in “inversePole” function 2015-03-29 19:16:45 +00:00
Tias Maiti 0e7325b27d added function — “inversePole” axis rotated according to orientation (using crystal symmetry to ensure location falls into SST) 2015-03-28 07:43:49 +00:00
Martin Diehl 151d4ff75b fixed bug (crash) in case (meaningless) strings found after part or section key.
DAMASK itself is fine with it, and it can be used for commenting.
thanks to B. Bode for figuring out
2015-03-27 16:23:21 +00:00