Commit Graph

784 Commits

Author SHA1 Message Date
Martin Diehl 0292e8fcc7 preparing transition to Geom and Table classes 2019-12-08 11:11:02 +01:00
Martin Diehl 871ff4c218 use geom class 2019-12-08 09:31:56 +01:00
Martin Diehl 12564557e6 using central functionality 2019-12-08 09:18:15 +01:00
Martin Diehl 592878d364 need to invoke function 2019-11-25 17:29:13 +01:00
Martin Diehl 3e8518d861 following prospector guidelines 2019-11-24 19:30:00 +01:00
Martin Diehl c9f9f7c681 pack causes trouble with tests .. 2019-11-24 19:02:19 +01:00
Martin Diehl b2cdabd009 getting rid of shell scripts 2019-11-24 18:25:53 +01:00
Martin Diehl 816e86ae5f phasing out python shell scripts 2019-11-24 15:13:26 +01:00
Martin Diehl 8186be6293 compress functionality should be part of the geom class
automated decision is base on heuristic whether compression is memory
efficient
2019-11-24 14:27:24 +01:00
Martin Diehl 6060abb375 cleaning 2019-11-24 09:10:47 +01:00
Martin Diehl dfb95df689 migrating shell scripts to python class 2019-11-22 21:48:41 +01:00
Martin Diehl a2e4917d3b not needed for DADF5 2019-10-20 19:25:09 +02:00
Philip Eisenlohr bffeaa980d restored Martin's logic, not clear why seemed to be broken with PE's former tests... 2019-06-03 14:43:23 -04:00
Philip Eisenlohr 8d52a3d52a polishing of geom_rescale; adopted modified testing reference 2019-06-03 14:15:23 -04:00
Philip Eisenlohr 2870fdb25b fixed buggy version 2019-06-03 13:39:45 -04:00
Philip Eisenlohr 89e4bc800c removed default size to adjust to changes in geom-class 2019-06-03 13:38:48 -04:00
Philip Eisenlohr 60031cc806 changed periodic option to reflect to better reflect what happens 2019-06-03 13:35:37 -04:00
Philip Eisenlohr 7ea417d585 rotated geometry maintains center of gravity 2019-06-03 13:30:14 -04:00
Martin Diehl 615ff4ed06 [skip ci] vectorized 2019-05-31 23:26:32 +02:00
Martin Diehl 02671c5c03 bugfix
shoud now work for any possible combination of new and old grid and
offset
2019-05-31 15:58:47 +02:00
Martin Diehl 979145f023 vectorized 2019-05-31 10:27:26 +02:00
Martin Diehl 46f0ad052e direct support for vtk output
- geom_check can now handle multiple files
- microstructure index is stored as integer in vtk file
2019-05-30 15:35:45 +02:00
Martin Diehl 08052737cf if grid is an option, it is a tuple
tuples do not have the prod() function
2019-05-30 14:28:31 +02:00
Martin Diehl c2a5f37818 round to reasonable precision
without symmetry, there are 36000**3 = 46656000000000 orientations
2019-05-30 14:11:54 +02:00
Martin Diehl bf60cffab5 cleaning 2019-05-30 14:07:49 +02:00
Martin Diehl d0c7f8b934 texture is typically the more interesting information
therefore, but it to the top
2019-05-30 14:05:45 +02:00
Martin Diehl 8380071564 using geom class
- dropped the use of the material class as it does not allow to have
empty phase and crystallite. The material.config class needs a severe
refurbishing (no crystallite, use orderedDict instead of hand written
solution, drop of texture components). Probably best solution is to
postpone this until we have a yaml/json reader for Fortran.
2019-05-30 13:30:38 +02:00
Martin Diehl 7d07a3752f polishing 2019-05-30 13:30:18 +02:00
Martin Diehl 461611cde7 polishing 2019-05-30 11:26:47 +02:00
Martin Diehl 49c3903cc7 explicit loop for simpler code
- no invalid combintations any more (allow to move the original
microstructure out of the new canvas)
- handling of origin needs discussion. When we want to recover the old
behavior, the origin might be located outside of the new geometry
2019-05-30 11:26:07 +02:00
Martin Diehl e974bb9c43 similar structure for building blocks 2019-05-30 10:45:17 +02:00
Martin Diehl 510b55df50 several improvements
- more error checking
- order of points can be arbitrary also for microstructure input
- grouping of same orientation/phase combinations
2019-05-30 10:33:01 +02:00
Martin Diehl 931fa9d36a standardized and cleaned
-write to file if given
-type casting is done in the geom class
2019-05-30 10:20:07 +02:00
Martin Diehl 07276d511c modern python formatting
- 2 digits should be precise enough for euler angles
- no need to pad grain ID with leading zeros
2019-05-30 10:03:55 +02:00
Martin Diehl 73df615ff3 numpy meshgrid can do this now 2019-05-30 09:45:30 +02:00
Martin Diehl 4e0e5a2329 new python formatting style 2019-05-30 09:41:22 +02:00
Martin Diehl f30eda0267 no need to loop over files
will procude the same file over and over again
2019-05-30 09:32:37 +02:00
Philip Eisenlohr cdc8338347 full (not periodic) mirroring is geom_mirror default behavior 2019-05-29 20:22:29 -06:00
Philip Eisenlohr d79f0c6290 replace geom_canvas --blank with geom_fromScratch 2019-05-29 20:02:06 -06:00
Martin Diehl fd9801ba09 StringIO not needed 2019-05-29 19:44:38 +02:00
Martin Diehl d7e8a66746 polishing 2019-05-29 14:18:11 +02:00
Martin Diehl 16bd5294aa loop order as intented 2019-05-29 14:06:39 +02:00
Martin Diehl 78f30684f8 moderized
needs some polishing with respect to array orders
2019-05-29 09:40:56 +02:00
Martin Diehl 6836a2eae8 better readable 2019-05-29 08:04:01 +02:00
Martin Diehl dfc2b47abc better readable 2019-05-29 08:01:00 +02:00
Martin Diehl 8ee23b37b2 should not be part of the repo 2019-05-29 07:52:44 +02:00
Martin Diehl bb6f54963a save some memory (avoid copies if not needed) 2019-05-29 07:49:43 +02:00
Martin Diehl 9f68923038 restored old behavior
save some ressources by avoiding copies.
much slower than old version, better cast formula into meshgrid again
2019-05-29 07:38:11 +02:00
Martin Diehl 2eb964b1ea simplified
needs some manual checking and proper test
2019-05-28 23:49:11 +02:00
Martin Diehl 100a2031d3 [skip ci] no white space needed 2019-05-28 07:55:24 +02:00
Philip Eisenlohr 1f56ac6a4a streamlining and bugfixing of geom-class 2019-05-27 22:45:34 -06:00
Martin Diehl b69f0efbbc improved and simplified reporting 2019-05-27 22:00:26 +02:00
Martin Diehl 59c6c5cfe4 not needed anymore
essentially, (gauss) is an Euler angle triplet
2019-05-27 10:49:50 +02:00
Martin Diehl 6e06764e2d using (enhanced) central functionality 2019-05-27 08:38:02 +02:00
Martin Diehl d9ab87cfde crystallite will be removed soon, error handling is done by geom class 2019-05-27 08:35:24 +02:00
Martin Diehl b5cec797c0 cleaned 2019-05-26 23:03:31 +02:00
Martin Diehl c8dfba89e5 using class
still a very complex script
2019-05-26 22:49:05 +02:00
Martin Diehl 15d5a7ae28 don't access attributes directly 2019-05-26 22:08:14 +02:00
Martin Diehl f251cdb746 simplified 2019-05-26 22:07:50 +02:00
Martin Diehl af493cf9fd using class
needs more memory, but should be faster and is better readable
2019-05-26 21:32:08 +02:00
Martin Diehl 99da46fda8 polished 2019-05-26 20:36:41 +02:00
Martin Diehl 657a30c2f5 using new functionality 2019-05-26 18:51:27 +02:00
Martin Diehl feb2340935 self-reporting functionality for updating 2019-05-26 17:58:54 +02:00
Martin Diehl 34f7bbe2a0 'blank' option does not fit to flow of script
seeds_fromRandom -N 1 | geom_fromVoronoiTessellation -g 30 30 30 -s 1 1 1 > file.geom
or a few lines of python code give the same results
2019-05-26 13:06:22 +02:00
Martin Diehl e7b8ae08d0 polishing 2019-05-26 12:14:48 +02:00
Martin Diehl 974f67ffdc no frills 2019-05-26 12:06:51 +02:00
Martin Diehl be3513d1e0 polishing.
python imports follow PEP8
2019-05-26 09:49:56 +02:00
Martin Diehl a242382bed Merge branch 'geometry-class' of magit1.mpie.de:/damask/DAMASK into geometry-class 2019-05-26 09:19:29 +02:00
Philip Eisenlohr b13aa799c3 updated error message 2019-05-25 17:00:41 +02:00
Martin Diehl c89d344236 polishing 2019-05-25 13:51:05 +02:00
Martin Diehl 2b7d95f800 was accidently commited
gives different results due to interpolation from scipy
2019-05-25 12:09:09 +02:00
Martin Diehl c92969787a geom Class was updated 2019-05-25 11:56:06 +02:00
Martin Diehl 94f85b7f33 better readable 2019-05-25 10:45:58 +02:00
Martin Diehl fc1f65c34e works for dtype='float' 2019-05-25 10:36:46 +02:00
Martin Diehl 875643c363 same style 2019-05-25 10:24:45 +02:00
Martin Diehl 17eb0d1b20 using new class 2019-05-25 08:48:44 +02:00
Martin Diehl 4788fc6046 making use of new class
@philip: 1D arrangement needed?
2019-05-25 08:37:02 +02:00
Martin Diehl 6c7f7c77da specifying non-existing or invalid files is an user error
this is the standard behavior for common unix tools, no need to make an
exception here
2019-05-25 08:24:32 +02:00
Martin Diehl cf374a04dc using new class 2019-05-25 08:21:00 +02:00
Martin Diehl 420abfa162 use new class 2019-05-24 22:34:27 +02:00
Philip Eisenlohr eb13fbc0ce streamlined geom-info reporting; added --float option to some scripts; hardened against NaN; "microstructures" now reports uniques not max 2019-05-23 13:03:24 -04:00
Philip Eisenlohr e6cec6ecbe added option to reverse inside/outside of primitive body 2019-05-23 12:49:03 -04:00
Martin Diehl ed7423a3d6 bug fixes 2019-03-10 08:16:01 +01:00
Martin Diehl 67619fa92a consistent definition of axis angle 2019-03-09 20:18:28 +01:00
Martin Diehl b84d4f1b6a improved error handling/clearer messages 2019-03-05 10:58:57 +01:00
Philip Eisenlohr e030038b73 [skip ci] added --blank option to create fresh canvas (from nothing) 2019-02-27 19:37:38 -05:00
Eureka Pai e401c21266 dropped obsolete option --inplace from geom_check 2019-02-25 18:30:45 -05:00
Martin Diehl e88182b007 improved converte, now with test
still needs to figure out how +P is handled
2019-02-24 14:39:34 +01:00
Martin Diehl 0d7fd587e3 direct translation from DREAM.3D to DAMASK geom
needs test
2019-02-24 12:59:10 +01:00
Martin Diehl 903edcd429 do not patronize the user, rather give hints 2019-02-24 10:31:08 +01:00
Martin Diehl d3ac3cc0f5 using new Orientation class 2019-02-24 08:34:20 +01:00
Martin Diehl 9dc8dff4b1 cleaning and adding compatibility layer 2019-02-23 22:35:04 +01:00
Martin Diehl a8e8b75cc0 use new rotation class 2019-02-23 22:13:24 +01:00
Martin Diehl fff377de7f initial simplification.
Should be able to generate from table containing either <microstructure>
or <texture> and <phase>
2019-02-23 22:06:31 +01:00
Martin Diehl b3455c825e transition to new orientation class
forward-backward conversion quite stable
2019-02-23 21:49:05 +01:00
Martin Diehl e4bb61c9d9 transition to new orientation class/DREAM.3D 2019-02-23 11:37:09 +01:00
Martin Diehl 93ae5cbd07 Merge remote-tracking branch 'origin/development' into 10-consistent-orientation-conversions-3 2019-02-22 23:05:36 +01:00
Satyapriya Gupta 3bec76e781 can now deal with 1x1x1 geoms 2019-02-19 12:06:46 -05:00
Martin Diehl 25727bfa52 using CamelCase 2019-02-19 10:32:18 +01:00
Martin Diehl 27ebe1f665 improved documentation 2019-02-17 08:17:40 +01:00
Philip Eisenlohr dc133344b6 [skip ci] migrated to python3 compatibility 2019-02-14 18:44:06 -05:00
Philip Eisenlohr 742d58cfce added ASCIItable tests to CI pipelining 2019-02-14 18:24:09 -05:00
Martin Diehl 608852df83 rotation paper has angle as last component 2019-02-12 10:58:38 +01:00
Martin Diehl 97ac437686 more user friendly constructors 2019-02-12 08:14:27 +01:00
Martin Diehl ef3fc0b58a bugfix: wrong array indexing
rotation of meshgrid tuple implemented
2019-02-12 07:42:46 +01:00
Martin Diehl 48b0307fab using new rotation class
cannot rotate matrices (3,3) and (3,3,3,3) at the moment
2019-02-12 00:27:13 +01:00
Martin Diehl da115ca9d4 probably never used and outdated (python2.7)
doing the same conversion via DREAM.3D will be available soon
2019-01-16 17:51:37 +01:00
Martin Diehl c5dabbb68f correct comment sign
the # indicates the end of a list
2019-01-09 16:31:00 +01:00
Martin Diehl 0dca8d2740 compatible to python 3 and mentat >= 2017 2019-01-09 16:28:21 +01:00
Philip Eisenlohr 9bdd4d1d68 added <!skip> line to stop config parser from trying to interpret rest of geom description---huge speedup!! 2018-12-20 17:22:29 -05:00
Martin Diehl 5d7f930592 math.isclose does not exist for older versions
np.isclose does the same
2018-12-17 20:04:16 +01:00
Martin Diehl e8f4dc4c9f Merge branch 'orientationClass_with_negative_P' into development 2018-12-06 07:26:08 +01:00
Martin Diehl ee7e4ee0d9 python3 has different encoding syntax 2018-12-06 06:27:07 +01:00
Philip Eisenlohr a6d4c73de0 added list of map and introduced "quat" keyword in quaternion init 2018-12-05 10:20:05 -05:00
Philip Eisenlohr c0f7ae2798 updated scripts that still used formerly valid object properties of quaternions 2018-12-05 09:07:29 -05:00
Philip Eisenlohr 1d7172c971 adopted more intutitive alternative of P=-1 from Rowenhorst_etal2015 2018-12-04 17:05:35 -05:00
Martin Diehl 7c1e2e256c os.urandom returns byte, not string in python3 2018-11-24 10:07:47 +01:00
Martin Diehl d53b01ab56 also works for python3 2018-11-18 08:04:52 +01:00
Martin Diehl 015e819d4c python3 does not allow to compare tuple/list with int 2018-11-17 09:29:05 +01:00
Martin Diehl 82861e80bc more python3 related changes 2018-11-17 08:46:58 +01:00
Martin Diehl 558745b548 explicitly require python3
on older systems, python3 tpyically exists but python2 is the defaul
2018-11-17 08:12:12 +01:00
Martin Diehl 50f880afd1 more scripts working with python3 2018-11-16 19:32:17 +01:00
Martin Diehl 9922f5f646 adjusted to python3
translate is more complicated now:
https://stackoverflow.com/questions/41708770
2018-11-16 12:23:45 +01:00
Martin Diehl a3647cc587 more files with confirmed python3 compatibility 2018-11-16 09:03:12 +01:00
Martin Diehl e9e3fef8d4 more python3 compatible scripts 2018-11-15 16:40:54 +01:00
Martin Diehl a00d15b889 geom files are not labeled 2018-09-29 11:18:35 +02:00
Martin Diehl 8616a92309 unused module 2018-07-20 03:50:07 +02:00
Martin Diehl 24d1528e04 on the way to full python 3 compatibility 2018-07-20 03:31:46 +02:00
Martin Diehl 784ae28dbb now working with python 3 2018-07-20 00:39:50 +02:00
Martin Diehl 9821654aae iteritems does not exist in python3 anymore
items also works for python2 (might be slower though)
2018-07-19 16:16:10 +02:00
Philip Eisenlohr 1b12457fe6 vicinityOffset to specific triggering IDs instead of just any other ID 2018-03-30 11:48:02 -04:00
Philip Eisenlohr 0570a49ed5 fixed broken logic of restoring and preventing immutable microstructures 2018-03-27 16:53:49 -04:00
Philip Eisenlohr 2c3eae6bf0 fixed tests and bug for very small unit cube fractions when grid is also small 2018-03-07 18:59:27 -05:00
Philip Eisenlohr 32c34457c2 direct selection of valid seed coordinates within subfraction of unit cube instead of check and repeat 2018-03-07 17:45:22 -05:00
Philip Eisenlohr f5177b6d2d [skip ci] added option for non-periodic geometries 2018-02-20 10:20:35 -05:00
Martin Diehl ba3a4e1254 indicating vectors with 1_, ..., n_ is standard now, "euler" also (more or less) 2018-02-05 17:34:08 +01:00
Martin Diehl 4dfb52c792 unfinished HDF5 should not be part of the next release 2017-11-21 10:23:50 +01:00
Franz Roters eddc2a6acf numpy actually not needed 2017-10-20 10:17:08 +02:00
Franz Roters 0c24f113c1 split overlong line 2017-10-20 10:14:15 +02:00
Franz Roters 26b8788c06 script to colocate 2D ang files into one §D file and optionally creat geometry and Paraview files 2017-10-20 09:36:57 +02:00
Philip Eisenlohr ff072ae3c4 fixed bug (lost orgin info) 2017-08-23 15:14:22 -04:00
Philip Eisenlohr 9b6e092b5c changed location where script appends itself to info trail
used to be sometimes at top, sometimes at bottom; now always after predecessor and above standard geom header
2017-08-23 14:09:33 -04:00
Philip Eisenlohr f825e91bf1 script to straighten numbering in geom 2017-08-23 14:08:11 -04:00
Philip Eisenlohr 12fed7a38f added option to use seed coordinates that are not normalized to a unit cube 2017-08-16 16:24:45 -04:00
Philip Eisenlohr 4eff7cfdd8 fixed wrong name for "pos" options destination 2017-08-15 16:11:21 -04:00
Philip Eisenlohr 1a423617c2 combined assignement of curvature exponent to deal with negative dimensions 2017-08-03 12:12:47 -04:00
Philip Eisenlohr 84a3885af8 negated option from "voxelspace" to "realspace".
introduced logarithmic sense of curvature exponents, additional polishing
2017-08-03 12:08:51 -04:00
Martin Diehl e5af0630fe gaussian filter (wrapper no ndimage) 2017-05-29 10:33:05 +02:00
Martin Diehl 691f338f5d executable bit got lost 2017-05-19 09:33:58 +02:00
Franz Roters ed85ce5bdb changed argument handling in line with other scripts
now also works with stdin/out
2017-04-28 12:36:10 +02:00