bugpyFormex - Bugs: bug #49256, Bifmesh issues

 
 

bug #49256: Bifmesh issues

Submitted by:  None
Submitted on:  Mon 03 Oct 2016 05:25:19 PM UTC  
 
Category: PluginsSeverity: 3 - Normal
Item Group: Functionality errorStatus: Fixed
Privacy: PublicAssigned to: None
Open/Closed: Closed

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Mon 03 Oct 2016 05:27:55 PM UTC, comment #3:

Fixed in 403c57c.

Benedict Verhegghe <bverheg>
Project Administrator
Mon 03 Oct 2016 05:25:19 PM UTC, comment #2:

This item has been reassigned from the project pyFormex support tracker to your tracker.

The original report is still available at support #109157

Following are the information included in the original report:

[field #0] Item ID: 109157
[field #1] Group ID: 10866
[field #2] Open/Closed: Open
[field #3] Severity: 3 - Normal
[field #4] Privacy: Private
[field #7] : Unknown support Field Display Type
[field #8] : Unknown support Field Display Type
[field #9] Category: Plugins
[field #10] Submitted by: None
[field #11] Assigned to: None
[field #12] Submitted on: Mon 03 Oct 2016 06:14:05 PM CEST
[field #13] Summary: Bifmesh issues
[field #14] Original Submission: I'm new to Python and Pyformex. I have tried running though the Bifmesh plugin example but it gives me errors and does not complete the meshing step (errors listed below). Is there anything I can do to help complete the meshing process?

elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison

`Called from:` /usr/local/lib/python2.7/dist-packages/pyformex/gui/draw.py `line:` 773
Central Point = [-1.92753589 0.94010758 -0.1379855 ]
Branch control lines:
0, 0
[[ -1.96555257 6.90520096 0. ]
[ 19.08426476 10.4637661 0. ]]
0, 1
[[ 2.61836171 0.87373471 0. ]
[ 19.14457893 1.2959373 0. ]]
1, 0
[[ 2.61836171 0.87373471 0. ]
[ 19.08426476 -1.59916639 0. ]]
1, 1
[[ -1.84492326 -6.30370998 0. ]
[ 19.02395058 -12.6970644 0. ]]
2, 0
[[ -1.84492326 -6.30370998 0. ]
[-34.29421234 -4.61489964 0. ]]
2, 1
[[ -1.96555257 6.90520096 0. ]
[-33.93232346 7.50834751 0. ]]
[('nslice', [10, 10, 10])]
1
[('nslice', [10, 10, 10])]
..

pyFormex Warning
================
elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison

`Called from:` /usr/local/lib/python2.7/dist-packages/pyformex/geometry.py `line:` 222
[('nseeds0', '[5,3 ]'), ('ratios0', '[0.3, 0.4]'), ('nseeds1', '[5,3 ]'), ('ratios1', '[0.3, 0.4]'), ('nseeds2', '[5,3 ]'), ('ratios2', '[0.3, 0.4]')]
# of seeds in branches: [11, 11, 11]
[('nseeds0', '[5,3 ]'), ('ratios0', '[0.3, 0.4]'), ('nseeds1', '[5,3 ]'), ('ratios1', '[0.3, 0.4]'), ('nseeds2', '[5,3 ]'), ('ratios2', '[0.3, 0.4]')]
[('domain', 'Lumen')]
Meshing Lumen
..

pyFormex Warning
================
comparison to `None` will result in an elementwise object comparison in the future.

`Called from:` /usr/local/lib/python2.7/dist-packages/pyformex/plugins/vascularsweepingmesher.py `line:` 213
..

pyFormex Warning
================
comparison to `None` will result in an elementwise object comparison in the future.

`Called from:` /usr/local/lib/python2.7/dist-packages/pyformex/plugins/vascularsweepingmesher.py `line:` 88
..

pyFormex Warning
================
using a non-integer number instead of an integer will result in an error in the future

`Called from:` /usr/local/lib/python2.7/dist-packages/pyformex/plugins/vascularsweepingmesher.py `line:` 227
# sections= 12, # inner quad reg = 4, # trans quad reg = 8, # boundary-layer quad reg = 8
--this vessel BIFURCATES both at FIRST AND LAST section
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/pyformex/plugins/bifmesh_menu.py", line 1041, in example
sweepingMesher()
File "/usr/local/lib/python2.7/dist-packages/pyformex/plugins/bifmesh_menu.py", line 671, in sweepingMesher
vmesh, smesh=meshBranch(branch[0], branch[1], longp, longc, longr, longbl)
File "/usr/local/lib/python2.7/dist-packages/pyformex/plugins/bifmesh_menu.py", line 596, in meshBranch
in_block = vsm.structuredHexMeshGrid(nlong,ncirc,ncirc,isophex='hex64')
File "/usr/local/lib/python2.7/dist-packages/pyformex/plugins/vascularsweepingmesher.py", line 72, in structuredHexMeshGrid
xh0= concatenate([xh0, xh0+1], axis=1)#first cell
IndexError
:
axis 1 out of bounds [0, 1)
/usr/local/lib/python2.7/dist-packages/pyformex/data/bifurcation.off
Reading .OFF /usr/local/lib/python2.7/dist-packages/pyformex/data/bifurcation.off
Read 16285 nodes and 32352 elems
Central Point = [-1.92753589 0.94010758 -0.1379855 ]
Branch control lines:
0, 0
[[ -1.96555257 6.90520096 0. ]
[ 19.08426476 10.4637661 0. ]]
0, 1
[[ 2.61836171 0.87373471 0. ]
[ 19.14457893 1.2959373 0. ]]
1, 0
[[ 2.61836171 0.87373471 0. ]
[ 19.08426476 -1.59916639 0. ]]
1, 1
[[ -1.84492326 -6.30370998 0. ]
[ 19.02395058 -12.6970644 0. ]]
2, 0
[[ -1.84492326 -6.30370998 0. ]
[-34.29421234 -4.61489964 0. ]]
2, 1
[[ -1.96555257 6.90520096 0. ]
[-33.93232346 7.50834751 0. ]]
[('nslice', [10, 10, 10])]
[('nseeds0', '[5,3 ]'), ('ratios0', '[0.3, 0.4]'), ('nseeds1', '[5,3 ]'), ('ratios1', '[0.3, 0.4]'), ('nseeds2', '[5,3 ]'), ('ratios2', '[0.3, 0.4]')]
# of seeds in branches: [11, 11, 11]
[('nseeds0', '[5,3 ]'), ('ratios0', '[0.3, 0.4]'), ('nseeds1', '[5,3 ]'), ('ratios1', '[0.3, 0.4]'), ('nseeds2', '[5,3 ]'), ('ratios2', '[0.3, 0.4]')]
[('domain', 'Lumen')]
Meshing Lumen
# sections= 12, # inner quad reg = 4, # trans quad reg = 8, # boundary-layer quad reg = 8
--this vessel BIFURCATES both at FIRST AND LAST section
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/pyformex/plugins/bifmesh_menu.py", line 1041, in example
sweepingMesher()
File "/usr/local/lib/python2.7/dist-packages/pyformex/plugins/bifmesh_menu.py", line 671, in sweepingMesher
vmesh, smesh=meshBranch(branch[0], branch[1], longp, longc, longr, longbl)
File "/usr/local/lib/python2.7/dist-packages/pyformex/plugins/bifmesh_menu.py", line 596, in meshBranch
in_block = vsm.structuredHexMeshGrid(nlong,ncirc,ncirc,isophex='hex64')
File "/usr/local/lib/python2.7/dist-packages/pyformex/plugins/vascularsweepingmesher.py", line 72, in structuredHexMeshGrid
xh0= concatenate([xh0, xh0+1], axis=1)#first cell
IndexError
:
axis 1 out of bounds [0, 1]
[field #16] Item Group: None
[field #17] Status: None
[field #18] Component Version: None
[field #19] Operating System: GNU/Linux
[field #20] Reproducibility: None
[field #21] Size (loc): None
[field #22] Fixed Release: None
[field #23] Planned Release: None
[field #24] Effort: 0.00
[field #28] Priority: 5 - Normal
[field #31] Percent Complete: 0%
[field #33] Release: None
[field #36] Originator Email: b.oreilly1@nuigalway.ie
[field #58] Custom Select Box #1: None
[field #59] Custom Select Box #2: None
[field #60] Custom Select Box #3: None
[field #61] Custom Select Box #4: None
[field #62] Custom Select Box #5: None
[field #63] Custom Select Box #6: None
[field #64] Custom Select Box #7: None
[field #65] Custom Select Box #8: None
[field #66] Custom Select Box #9: None
[field #67] Custom Select Box #10: None

Benedict Verhegghe <bverheg>
Project Administrator
Mon 03 Oct 2016 05:25:19 PM UTC, comment #1:

The warnings can be ignored: they result from a newer numpy version, and will be dealt with in future releases.

The error in /usr/local/lib/python2.7/dist-packages/pyformex/plugins/vascularsweepingmesher.py is a bug in pyFormex (which probably was ignored with older numpy versions).

If you have access to the source files, you can fix the bug by changing the file /usr/local/lib/python2.7/dist-packages/pyformex/plugins/vascularsweepingmesher.py in line 72. Just remove the ',axis=1' part to make that line read:

xh0= concatenate([xh0, xh0+1])#first cell

Alternatively, you can install a newer (development) version of pyFormex from the git sources. The bug was fixed in commit 403c57c.

Benedict Verhegghe <bverheg>
Project Administrator
Mon 03 Oct 2016 05:25:19 PM UTC, original submission:

I'm new to Python and Pyformex. I have tried running though the Bifmesh plugin example but it gives me errors and does not complete the meshing step (errors listed below). Is there anything I can do to help complete the meshing process?

elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison

`Called from:` /usr/local/lib/python2.7/dist-packages/pyformex/gui/draw.py `line:` 773
Central Point = [-1.92753589 0.94010758 -0.1379855 ]
Branch control lines:
0, 0
[[ -1.96555257 6.90520096 0. ]
[ 19.08426476 10.4637661 0. ]]
0, 1
[[ 2.61836171 0.87373471 0. ]
[ 19.14457893 1.2959373 0. ]]
1, 0
[[ 2.61836171 0.87373471 0. ]
[ 19.08426476 -1.59916639 0. ]]
1, 1
[[ -1.84492326 -6.30370998 0. ]
[ 19.02395058 -12.6970644 0. ]]
2, 0
[[ -1.84492326 -6.30370998 0. ]
[-34.29421234 -4.61489964 0. ]]
2, 1
[[ -1.96555257 6.90520096 0. ]
[-33.93232346 7.50834751 0. ]]
[('nslice', [10, 10, 10])]
1
[('nslice', [10, 10, 10])]
..

pyFormex Warning
================
elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison

`Called from:` /usr/local/lib/python2.7/dist-packages/pyformex/geometry.py `line:` 222
[('nseeds0', '[5,3 ]'), ('ratios0', '[0.3, 0.4]'), ('nseeds1', '[5,3 ]'), ('ratios1', '[0.3, 0.4]'), ('nseeds2', '[5,3 ]'), ('ratios2', '[0.3, 0.4]')]
# of seeds in branches: [11, 11, 11]
[('nseeds0', '[5,3 ]'), ('ratios0', '[0.3, 0.4]'), ('nseeds1', '[5,3 ]'), ('ratios1', '[0.3, 0.4]'), ('nseeds2', '[5,3 ]'), ('ratios2', '[0.3, 0.4]')]
[('domain', 'Lumen')]
Meshing Lumen
..

pyFormex Warning
================
comparison to `None` will result in an elementwise object comparison in the future.

`Called from:` /usr/local/lib/python2.7/dist-packages/pyformex/plugins/vascularsweepingmesher.py `line:` 213
..

pyFormex Warning
================
comparison to `None` will result in an elementwise object comparison in the future.

`Called from:` /usr/local/lib/python2.7/dist-packages/pyformex/plugins/vascularsweepingmesher.py `line:` 88
..

pyFormex Warning
================
using a non-integer number instead of an integer will result in an error in the future

`Called from:` /usr/local/lib/python2.7/dist-packages/pyformex/plugins/vascularsweepingmesher.py `line:` 227
# sections= 12, # inner quad reg = 4, # trans quad reg = 8, # boundary-layer quad reg = 8
--this vessel BIFURCATES both at FIRST AND LAST section
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/pyformex/plugins/bifmesh_menu.py", line 1041, in example
sweepingMesher()
File "/usr/local/lib/python2.7/dist-packages/pyformex/plugins/bifmesh_menu.py", line 671, in sweepingMesher
vmesh, smesh=meshBranch(branch[0], branch[1], longp, longc, longr, longbl)
File "/usr/local/lib/python2.7/dist-packages/pyformex/plugins/bifmesh_menu.py", line 596, in meshBranch
in_block = vsm.structuredHexMeshGrid(nlong,ncirc,ncirc,isophex='hex64')
File "/usr/local/lib/python2.7/dist-packages/pyformex/plugins/vascularsweepingmesher.py", line 72, in structuredHexMeshGrid
xh0= concatenate([xh0, xh0+1], axis=1)#first cell
IndexError
:
axis 1 out of bounds [0, 1)
/usr/local/lib/python2.7/dist-packages/pyformex/data/bifurcation.off
Reading .OFF /usr/local/lib/python2.7/dist-packages/pyformex/data/bifurcation.off
Read 16285 nodes and 32352 elems
Central Point = [-1.92753589 0.94010758 -0.1379855 ]
Branch control lines:
0, 0
[[ -1.96555257 6.90520096 0. ]
[ 19.08426476 10.4637661 0. ]]
0, 1
[[ 2.61836171 0.87373471 0. ]
[ 19.14457893 1.2959373 0. ]]
1, 0
[[ 2.61836171 0.87373471 0. ]
[ 19.08426476 -1.59916639 0. ]]
1, 1
[[ -1.84492326 -6.30370998 0. ]
[ 19.02395058 -12.6970644 0. ]]
2, 0
[[ -1.84492326 -6.30370998 0. ]
[-34.29421234 -4.61489964 0. ]]
2, 1
[[ -1.96555257 6.90520096 0. ]
[-33.93232346 7.50834751 0. ]]
[('nslice', [10, 10, 10])]
[('nseeds0', '[5,3 ]'), ('ratios0', '[0.3, 0.4]'), ('nseeds1', '[5,3 ]'), ('ratios1', '[0.3, 0.4]'), ('nseeds2', '[5,3 ]'), ('ratios2', '[0.3, 0.4]')]
# of seeds in branches: [11, 11, 11]
[('nseeds0', '[5,3 ]'), ('ratios0', '[0.3, 0.4]'), ('nseeds1', '[5,3 ]'), ('ratios1', '[0.3, 0.4]'), ('nseeds2', '[5,3 ]'), ('ratios2', '[0.3, 0.4]')]
[('domain', 'Lumen')]
Meshing Lumen
# sections= 12, # inner quad reg = 4, # trans quad reg = 8, # boundary-layer quad reg = 8
--this vessel BIFURCATES both at FIRST AND LAST section
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/pyformex/plugins/bifmesh_menu.py", line 1041, in example
sweepingMesher()
File "/usr/local/lib/python2.7/dist-packages/pyformex/plugins/bifmesh_menu.py", line 671, in sweepingMesher
vmesh, smesh=meshBranch(branch[0], branch[1], longp, longc, longr, longbl)
File "/usr/local/lib/python2.7/dist-packages/pyformex/plugins/bifmesh_menu.py", line 596, in meshBranch
in_block = vsm.structuredHexMeshGrid(nlong,ncirc,ncirc,isophex='hex64')
File "/usr/local/lib/python2.7/dist-packages/pyformex/plugins/vascularsweepingmesher.py", line 72, in structuredHexMeshGrid
xh0= concatenate([xh0, xh0+1], axis=1)#first cell
IndexError
:
axis 1 out of bounds [0, 1]

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    Follow 7 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Mon 03 Oct 2016 05:30:10 PM UTCbverhegPrivacyPrivate=>Public
    Mon 03 Oct 2016 05:27:55 PM UTCbverhegCategoryNone=>Plugins
      Item GroupNone=>Functionality error
      StatusNone=>Fixed
      PrivacyPublic=>Private
      Open/ClosedOpen=>Closed
    Mon 03 Oct 2016 05:25:19 PM UTCbverhegReassign itempyFormex, sr #109157=>pyFormex, bug #49256

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