8cdc7c0b10
add xdmf wrapper generator for HDF5
...
Not recommended for large dataset due to potential memory leak currently plaguing Xdmf ilbrary.
2016-10-13 13:41:04 -04:00
ec59dfeec0
do not reshape data
...
since xdmf is not stable right now, there is no need to reshape the data to tie it to the mesh. comment them out for future reference
2016-10-13 13:22:37 -04:00
ace06fd0e1
skip dulplicated columns in ascii table
...
also add a todo list at the top
2016-10-13 11:33:38 -04:00
c311ac47ca
force using rectangular mesh
...
Paraview cannot handle large number of polyvertices using xdmf, forcing a meshed structure to by pass the problem.
2016-10-12 20:20:15 -04:00
ffcfe67c73
remove debug output, fix name handling error
2016-10-10 09:46:11 -04:00
7278605004
fix naming error
2016-10-09 19:13:44 -04:00
6450cb3003
fix syntax error
2016-10-09 19:12:45 -04:00
6eb111dc7c
add script convert ASCII table to HDF5
...
using H5Table
2016-10-09 19:01:38 -04:00
4e8bd83d4b
syntax error fix
2016-10-07 15:32:10 -04:00
5951b45259
only grain file type 1 seems to make sense (type 2 has average values).
...
For type one, data is fixed i.e. flexible labels are not useful
2016-10-06 15:22:05 +02:00
de88bebe99
handling defaults correctly for extend option
2016-10-06 12:14:07 +02:00
f78f89fb12
periodic microstructure needs to be updated per iteration (N).
...
now calling script twice gives the same result as one call with N=2.
results for N=1 are not affected
2016-10-05 15:24:37 +02:00
3abf0bc2d3
Merge branch 'development' of magit1.mpie.de:damask/DAMASK into miscImprovements
2016-09-27 06:22:52 +02:00
0ffd74d536
correct flag "data" for updated vtk_addRectilinearGridData
2016-09-26 16:32:39 -04:00
1d06e82700
grain circumference identification
...
fixed right most path selection criteria for grain circumference
2016-09-26 16:30:50 -04:00
5345b42d71
improved robustness against faulty RCB data
...
deals gracefully with duplicate segments, new option to export cleaned up RCB
2016-09-25 21:18:53 -04:00
fb23c49b41
should be executable
2016-09-24 15:58:13 +02:00
e20623845a
Merge branch 'development' of magit1.mpie.de:damask/DAMASK into miscImprovements
2016-09-22 16:14:07 +02:00
0f09a66b62
pyflake was complaining
2016-09-22 15:36:28 +02:00
f8901220ab
Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development
2016-09-22 15:34:28 +02:00
25103205a8
bug fix, adjust to options change of vtk_addXXXData
2016-09-21 22:01:16 +02:00
0f636bf6c3
not needed
2016-09-21 17:47:37 +02:00
4cd8fe7f36
indices should be integers (visible warning)
2016-09-21 17:45:23 +02:00
43457dcfc5
flexible selection of axes
2016-09-21 17:43:07 +02:00
4ccc0cf5a1
tool to mirror geometries (enforce periodicity on measured data)
2016-09-21 17:06:50 +02:00
1180c8bb88
Fix calculation of interfaceEnergy
2016-09-15 17:36:43 -04:00
f3308dbef6
replace scalar/vector option with data
...
vtk does not care 1D data array length
2016-09-14 19:59:26 -04:00
38d1a2c254
Merged branch development into development
2016-09-14 19:50:18 -04:00
eb69d6f4f1
Merged branch development into development
2016-09-14 19:42:15 -04:00
59c1eee16b
added possibility to restrict seed coordinates to fraction of unit box
2016-09-14 19:42:05 -04:00
ae16ccae61
need to use deep copy when converting np array to vtk array
...
for batch array conversion, it is necessary to use the deep copy to ensure numpy_support.numpy_to_vtk works as it should.
2016-09-14 15:06:00 -04:00
53d2df6058
vector support 1D vector with arbitrary lenght
...
simple hack to bypass the size check for vectors since vtk does not care the vector size.
2016-09-14 12:37:07 -04:00
804931db9e
force type cast index to int for numpy array
...
Force type casting indices into int array to avoid warning:
VisibleDeprecationWarning: using a non-integer number instead of an integer will result in an error in the future
For more info, see http://stackoverflow.com/questions/20084218/deprecation-warning-in-scikit-learn-svmlight-format-loader
2016-09-12 19:09:48 -04:00
77729f39e3
commenting last commit
2016-09-11 14:41:48 +02:00
06405bc251
fixed coordinate system convention to be right handed always instead of random left and right handed assignment
2016-09-10 16:39:25 -04:00
2daad7542e
added option for periodic averaging
2016-09-10 16:39:25 -04:00
ee322be870
use np.histogram2d, fixed list.append bug when using weight column
2016-09-09 16:17:00 -04:00
8c4767d58c
syntax fix
2016-09-09 07:28:54 -04:00
017c08a7bb
syntax fix
2016-09-09 07:28:31 -04:00
da538fbce9
speed up of VTK data transformation
2016-09-08 18:05:49 -04:00
c05307a273
Merge branch 'development' of magit1.mpie.de:damask/DAMASK into miscImprovements
2016-09-03 14:35:53 +02:00
a2f3839ca8
add missing numpy import
2016-09-02 14:37:15 -04:00
d9077805e4
Forced symetric tensor when adding tensor to vtk
...
VTK addTensor by default using the lower triangle to populate its tensor object. Enforcing the tensor to be symmetric to avoid necessary confusion when adding data (most stress/strain tensor should symmetric by default, so it should not affect the results)
2016-09-02 09:30:49 -04:00
20d1164e5d
add tensor support for vtk_addRectlinearGridData
2016-09-01 16:57:29 -04:00
6db0a42eae
addvtk data now support tensor type (9 components)
2016-09-01 12:47:26 -04:00
4b02a55f4d
explicit type casting from boolean to int
2016-08-30 16:08:47 -04:00
891ac4d585
fixed comma syntax error
2016-08-25 12:17:27 -04:00
55d6adf1b8
renamed to reflect more general nature of script
2016-08-25 12:15:41 -04:00
85abf84186
generalized to user-specified mapping function instead of hardwired avg
2016-08-25 12:15:03 -04:00
f984f1ebea
enable floating point data and corrected counting of microstructures
2016-08-24 16:05:50 -04:00
7710f4d444
hybridIA (stand alone script and DAMASK) need standard ASCII table
...
export of TSL OIM is similar to standard ASCII table, simply add correct header
including labels
2016-08-23 17:21:17 +02:00
c2b1499d84
Merge branch 'development' of magit1.mpie.de:damask/DAMASK into miscImprovements
2016-08-16 12:46:03 +02:00
64ac05fc26
removed left-over debug output
2016-08-11 14:24:40 -04:00
600731b15c
modernized, gracefully add NaN for out-of-bounds mapping
2016-08-11 14:23:29 -04:00
d239cab3ae
corrected help
2016-08-11 13:48:15 +02:00
a0567e8642
added FeatureID and right coordniates to table
2016-08-04 11:11:24 +02:00
ccc0ac35ac
copied from ang_toTable
2016-08-02 11:30:36 +02:00
6c82641713
added defaults (bugfix)
2016-08-01 16:43:14 +02:00
fa3387486d
clarified meaning of possible (global) rotation (lab/crystal frame)
2016-07-31 19:35:10 -04:00
79ff040426
sorting and clarification of help, shortening of output labels
2016-07-30 15:07:44 -04:00
23a57ec78f
reinstalled "NOQA" keyword for "import math"
2016-07-30 12:52:49 -04:00
ab3415d44e
polishing and rearrangement of code snippets
2016-07-30 12:46:00 -04:00
c3650a1b00
shebang got reverted
2016-07-30 08:20:57 +02:00
6a80c71c0b
Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development
2016-07-29 20:42:38 -04:00
304fdf1ebe
can deal with "veterans" and "newbies" meaning over ride existing with new
2016-07-29 20:41:15 -04:00
b39915afe1
Merged branch development into development
2016-07-29 17:51:16 -04:00
0bbf54e0e4
switched to string.format() method
2016-07-29 17:49:29 -04:00
afff0b8614
fixed STDOUT error
...
no files on command line translate to "filename" being empty list. Cannot test for filename[0] then...
2016-07-29 17:48:40 -04:00
2a0be6d232
Merge branch 'development' of magit1.mpie.de:damask/DAMASK into miscImprovements
2016-07-27 08:57:13 +02:00
1195593233
some casting was needed, corrected header
2016-07-25 19:39:09 +02:00
4d01e826c5
fixed typo in usage msg
2016-07-25 00:46:11 -04:00
99963ca1dd
Merged branch development into development
2016-07-24 19:19:03 -04:00
6f527b2af8
fixed upperCase typo in vtk_addPointcloudData call
2016-07-24 19:18:48 -04:00
03bb0b8a98
Merge branch 'development' of magit1.mpie.de:damask/DAMASK into miscImprovements
2016-07-18 19:36:47 +02:00
cd63a92733
using python 2.7 has shebang will also work on mac without symlink
...
unless someone uses the 6 year old python 2.6, this should be save
2016-07-18 19:35:35 +02:00
0a2d5e4c2a
add missing newline to header for postResult
2016-07-18 12:29:12 -04:00
325e153d3d
import of string not needed
2016-07-18 11:22:53 +02:00
e3f83b6d66
Merge branch 'development' of magit1.mpie.de:damask/DAMASK into miscImprovements
2016-07-18 11:22:12 +02:00
1b30b186f4
rootRelation keyword was still used
2016-07-18 06:17:22 +02:00
0c2b7782d4
reporting correct ID
2016-07-17 18:18:57 +02:00
40414c767c
like ang_toTable (not sure if both are needed anyway)
2016-07-15 21:03:10 +02:00
ce7cd36bf5
better be done with load case rotation
2016-07-15 20:23:20 +02:00
e8153ad196
corrected name
2016-07-15 15:48:53 +02:00
c792b73b4e
simplified
2016-07-15 14:52:48 +02:00
7d84b99710
bugfix: axis out of bounds for np.repeat, np.tile seems to be ok @Philip: pls check. autodoc friendly help
2016-07-15 10:34:17 +02:00
9e8adf731b
fixed buggy a.all() call
...
removed squaring of Laguerre weights (no clue why we considered this a good idea in the first place)
2016-07-07 15:23:01 -04:00
3ada327d3f
Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development
2016-07-04 21:43:33 +02:00
745c012088
fully adopted code from addDisplacement
2016-06-29 20:09:42 +02:00
f04b737e4c
Merge remote-tracking branch 'origin/development' into NoCoreModule
2016-06-29 16:11:07 +02:00
2c8427eb2a
seems to work now
2016-06-29 12:35:50 +02:00
9bf8b6221c
fixed fluct displacement
2016-06-29 12:11:07 +02:00
a64388355a
simplified
2016-06-29 11:02:49 +02:00
9ea6d3afd7
simplified FFT statements
2016-06-29 10:58:15 +02:00
cd5eddb444
Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development
2016-06-28 22:44:23 +02:00
af2404f0f8
no access out of bounds anymore (but incorrect results)
2016-06-27 23:27:30 +02:00
8307a4a9ab
trying to get the last things work without the core module
2016-06-27 19:38:12 +02:00
259ee072a6
Merge branch 'development' into NoCoreModule
2016-06-27 15:35:46 +02:00
b40cbd68bb
"-"sign caused reversed deformation mode
2016-06-27 15:19:02 +02:00
5fb5edc2ed
should be executable
2016-06-24 07:31:46 +02:00
aa9a8b21c7
lables is now a method, not an attribute
2016-05-18 18:31:54 +02:00
be99018ce3
Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development
2016-05-18 18:28:57 +02:00
a7c15b4c00
avoided quoting of "N of x" and "a to b".
2016-05-17 11:29:31 -04:00
12affbd240
simplified and corrected
2016-05-17 11:23:57 -04:00
a8765a963d
more fixing of old .labels use
2016-05-17 11:12:26 -04:00
66e06cf61f
shebang for python2 got lost
2016-05-17 16:41:38 +02:00
9103ee544b
Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development
2016-05-17 09:52:18 -04:00
fa3d8fa460
adopted description/simplified
2016-05-17 11:05:50 +02:00
8d6c601a45
fixed python flake complaints.
2016-05-16 20:17:17 -04:00
8e01247597
merged functionality of fillTable (change existing column values) into addCalculation. If labels already exist, they are altered. Otherwise, new columns are appended.
2016-05-16 20:06:13 -04:00
515b8ee457
reworked use of "labels" property to proper methods for access.
2016-05-16 19:55:06 -04:00
49b02ac1f2
label name inline with current scheme
2016-05-13 22:46:03 +02:00
fa5ebdd46b
added correct metavar
2016-05-13 09:43:56 +02:00
61c93bdbf4
adjusted help message for automated documentation
2016-05-12 08:54:34 +02:00
ba6889a54f
removed debug statement
2016-05-11 10:04:55 -04:00
0da55113f9
not needed anymore
2016-05-11 11:44:24 +02:00
a21e8cd863
usind explicitly python2 to run in environments with python 3 as default
2016-05-11 11:01:39 +02:00
5089d86b3d
sorting labels are now optional. uses existing labels (from left to right) for sorting if none specified.
2016-04-28 20:28:45 -04:00
d3a7ceff15
fixed serious bug regarding wrong reshaping order (was 'C' now 'F') of 3dim to 1dim and back.
2016-04-28 13:25:46 -04:00
426658eb36
Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development
2016-04-27 09:28:51 -04:00
b3e9877058
changed from "coords" to "pos"
...
remind user about (creating a new) nodal output file
2016-04-27 09:28:43 -04:00
d497503411
renamed options.coords/options.coordinates consistently to options.pos
2016-04-26 22:49:58 +02:00
0f0ca8cd71
Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development
2016-04-25 10:24:30 -05:00
36f41341ec
Merge branch 'SimplifiedvtkRectilinear' into development
2016-04-25 10:23:50 -05:00
c67fbe7653
distinguished between singular and plural in remark
2016-04-25 10:23:08 -05:00
7ed4ce859a
remove obsolete geom_frombarucentric script for microstructure reconstruction
2016-04-25 09:24:05 -04:00
c30c7714ad
hickup, probably from merge
2016-04-25 14:11:27 +02:00
26e5f97ff3
missing comma
2016-04-25 13:22:34 +02:00
2eb7ad7432
polishing
2016-04-25 12:59:15 +02:00
7ce208019c
Merge branch 'development' into miscImprovements
2016-04-25 12:36:02 +02:00
469ec4b00e
Merge branch 'development' of magit1.mpie.de:damask/DAMASK into miscImprovements
2016-04-25 12:33:06 +02:00
d6002bdb10
removed remaining argument line
2016-04-25 09:08:24 +02:00
e8afd57536
seems to work
2016-04-25 08:40:36 +02:00
26f437b507
fixed pointcloud issues for vtk < 7.0 (going back to old, non-XML format)
2016-04-25 08:28:00 +02:00
34aa11f197
finishing half-done renaming
2016-04-24 22:50:41 +02:00
db7c4bba45
same functionality can be accomplished with existing scripts.
...
addEuclideanDistance + geom_fromTable
(reLabel) + specify grid and size
2016-04-24 14:18:29 -05:00
2daa162da2
renamed option "position" to "seedposition". now uses util.report_geom.
2016-04-24 14:12:10 -05:00
4b7b473d2b
superseded by more modern vtk_* machinery
2016-04-24 13:46:25 -05:00
478acb96ce
exchanged by more modern vtk_* machinery...
2016-04-24 13:38:36 -05:00
88548cbb87
accidentally copied wrong writerType. now rectilinear...
2016-04-24 13:22:06 -05:00
8c0b0351cd
renamed "coordinates" option to "position". small additional polishing.
2016-04-24 13:12:18 -05:00
10e31e489a
new script to add arbitrary lines to ASCIItable header
2016-04-24 13:10:25 -05:00
b2b5f6b68c
removed useless check for croaking
2016-04-24 13:00:57 -05:00
219d489df4
Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development
2016-04-24 12:35:17 -05:00
94933514a1
removed "legacy" option. STDOUT reports most modern format available (ASCII XML for point cloud, VTK for rectilinear grid).
2016-04-24 12:34:01 -05:00
bd23f979f4
also not needed anymore
2016-04-24 19:27:19 +02:00
33391fcf5b
Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development
2016-04-24 18:58:32 +02:00
ac9a9cb6ac
scripts deemed useless
2016-04-24 18:56:13 +02:00
f1b5d40bac
now uses util.report_geometry. some additional modernizing on the fly.
2016-04-24 11:24:00 -05:00
c37c0a8ed9
added awareness for Laguerre weights
2016-04-24 11:22:54 -05:00
f42c316aa2
updated help
2016-04-24 10:14:16 -05:00
9e5a8d2391
modernized string formatting, updated help strings, using label_indexrange for data-slicing.
2016-04-24 10:09:28 -05:00
648c2dd1d3
Only read position coordinates for grid detection. Needs data_rewind before writing of (condensed due to readArray) head.
2016-04-24 09:22:07 -05:00
3b53d1bc82
polished option help messages
2016-04-22 14:20:36 -05:00
dffa119724
Added explicit option to force geom input format.
...
Added option to output legacy format.
Possible bug in VTK presently prevents XML output to STDOUT... (Have filed issue to VTK developers.)
2016-04-22 14:02:07 -05:00
57acaba63e
Missed out on putting the if..else statement as a bracketed group in a former commit. Next try of getting rid of {True: a,False: b}[choice] style...
2016-04-22 13:19:32 -05:00
382727f2d6
Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development
2016-04-22 13:13:42 -05:00
a1927f84c4
renamed "coordinates" option to "position".
...
added explicit choice to write out as legacy format.
2016-04-22 13:09:23 -05:00
a3da663931
piping was broken
2016-04-22 17:59:50 +02:00
c57c76085f
missing labels
2016-04-21 15:41:35 +02:00
28423d4b45
increment information got lost
2016-04-21 11:31:02 +02:00
8ec9243016
new label name
2016-04-21 11:06:39 +02:00
13e214fe18
added support for legacy VTK format
2016-04-18 15:08:29 -04:00
0bc7f36ee5
added (transparent) capability to deal with geom files.
2016-04-18 14:49:11 -04:00
24d029c7ed
speed up (x 5 to 10) identification of most frequent microstructure index
2016-04-15 18:54:09 -04:00
81f6530f52
changed default label of coordinates to "pos"
2016-04-15 18:27:23 -04:00
7567aae7c0
now deals with 1D, 2D, 3D. speed up of grid detection. "pos" as default coordinate label.
2016-04-15 18:25:56 -04:00
8ac40ced5a
coordinates of nodal or cell-centered values are always labelled "pos"
2016-04-15 18:23:35 -04:00
cbe9afb2b3
removed --mode option. script figures on its own.
2016-04-15 14:06:01 -04:00
3474800db1
switched coordinates default from "ipinitialcoords" (ugh) to "pos"
2016-04-15 14:04:10 -04:00
f040842ed4
superseded by addDisplacements
2016-04-15 07:41:55 -04:00
01ba11448c
small polishing of remark output regarding <3D vectors
2016-04-15 07:41:24 -04:00
91753d5322
more style related changes
2016-04-15 00:35:21 +02:00
5682d8f627
also not needed
2016-04-15 00:11:03 +02:00
6aa6b418ea
not needed (Philip has different names)
2016-04-15 00:08:01 +02:00
573d10f1e1
Merge branch 'development' into NoCoreModule
2016-04-15 00:05:38 +02:00
dbfd107b48
Add deformed configuration of given initial coordinates.
...
Operates on periodic three-dimensional x,y,z-ordered data sets.
Replaces 3Dvisualize..!
2016-04-14 17:53:48 -04:00
170d377092
much improved algorithm to speed up grain identification.
2016-04-13 19:36:24 -04:00
1994b5a4c1
removed debug messages
2016-04-13 19:29:04 -04:00
ea0bc80af9
modernized to reflect rectilinearGrid processing. Now supports vector data and in-place adding.
2016-04-13 18:03:40 -04:00
0b09ce31db
changed coordinate option to be consistent with rectilinearGrid.
2016-04-13 17:49:48 -04:00
feae2164fc
polishing and now explicitly closing input table.
2016-04-13 17:48:49 -04:00
6e2ca7d595
Removed hard requirement of 3D dataset. Fills in necessary dimensions.
2016-04-13 17:48:17 -04:00
70afa462b2
should work now with odd resolution as well
2016-04-11 20:25:24 +02:00
18f18aa4b9
detabbing
2016-04-11 19:55:55 +02:00
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
f483c6a404
Merge branch 'development' of magit1.mpie.de:damask/DAMASK into miscImprovements
2016-04-11 16:06:00 +02:00
d278d86f9d
long line
2016-04-11 13:24:43 +02:00
b1d714581c
Merge branch 'development' of magit1.mpie.de:damask/DAMASK into miscImprovements
2016-04-10 15:40:52 +02:00
b0496f20ca
grouped command line options.
...
removed functionality to add random second phase.
2016-04-08 17:47:02 -04:00
2354cd609a
small polishing of help.
...
added option to change output number format.
2016-04-08 17:46:06 -04:00
3e6d2710a3
added option to report probability density
2016-04-05 16:18:34 -04:00
e9ec497da6
fixed bug preventing files specified with full path to be treated properly
2016-04-05 16:17:55 -04:00
fcddf9345e
added option for non-uniform weights
2016-03-27 17:54:49 -04:00
7c72ede29d
now works properly for labels specified as index (instead of string)
2016-03-27 16:29:45 -04:00
0d93a47c71
Generate histogram of N bins in given data range.
2016-03-27 13:34:19 -04:00
97314619cc
corrections
2016-03-26 19:59:05 +01:00
7423c1a06a
not needed anymore
2016-03-24 18:47:11 +01:00
04d2148e61
will replace geom_fromAng (in combination with geom_fromTable)
2016-03-24 17:55:15 +01:00
ea28bc8f06
restored script for calculation of nodal positions
2016-03-24 16:19:49 +01:00
8b89063113
less core module
2016-03-24 14:19:00 +01:00
chen