Comments (12)
jonwright
commented on September 24, 2024
Thanks for the report. The problem is at the top of src/bldlib.py. Can you let me know what string you get from platform.machine() ? I am happy to get a pull request as I don't have this platform to test. Perhaps also issues in cImageD11.py.
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junyuewang
commented on September 24, 2024
Thanks!
import platform
platform.machine()
'mips64'
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jonwright
commented on September 24, 2024
Sorry - still working on this - should not be closed yet...
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jonwright
commented on September 24, 2024
Hopefully this is ready to test now. Can you try and see if it installs for you from git please?
python3 -m pip -v install git+https://github.com/FABLE-3DXRD/ImageD11.git
If that seems good, I would suggest to try a git checkout and then run the tests:
git clone https://github.com/FABLE-3DXRD/ImageD11.git
cd ImageD11/test
python run_tests.py
There should be a lot of output, but nothing looking like a test fail.
If it seems OK to you then I will try to remember how to upload to pypi ...
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junyuewang
commented on September 24, 2024
Thanks for the effort. I got a different error initially:
Command "/usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-w210hljv/h5py/setup.py';f=getattr(tokenize, 'open', open)(__file__);co
de=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-4b6jn96a/install-record.txt --single-versi
on-externally-managed --compile" failed with error code 1 in /tmp/pip-install-w210hljv/h5py/
Exception information:Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 143, in main
status = self.run(options, args) File "/usr/lib/python3/dist-packages/pip/_internal/commands/install.py", line
386, in run use_user_site=options.use_user_site,
File "/usr/lib/python3/dist-packages/pip/_internal/req/__init__.py", line 49, in install_given_reqs
**kwargs File "/usr/lib/python3/dist-packages/pip/_internal/req/req_install.py", line
791, in install spinner=spinner,
File "/usr/lib/python3/dist-packages/pip/_internal/utils/misc.py", line 723, in call_subprocess
% (command_desc, proc.returncode, cwd))pip._internal.exceptions.InstallationError: Command "/usr/bin/python3 -u -c "im
port setuptools, tokenize;__file__='/tmp/pip-install-w210hljv/h5py/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f
.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-4b6jn96a/install-record.txt --single-version-externally-managed --compile" fa
iled with error code 1 in /tmp/pip-install-w210hljv/h5py/
then I manually did apt install python3-h5py and run the command again, ImageD11 was successfully installed. The tests all failed:
python run_tests.py
Add "all" to command line to run all tests
HERE /home/junyue/Documents/xrd/ImageD11/test
Running suite for test_clean_mask
EEE
======================================================================
ERROR: test1 (test_clean_mask.test_clean_mask)
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_clean_mask.py", line 28, in test1
npx = cImageD11.clean_mask( self.src.astype(np.int8), testmask )
AttributeError: 'module' object has no attribute 'clean_mask'
======================================================================
ERROR: test_coo (test_clean_mask.test_clean_mask)
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_clean_mask.py", line 42, in test_coo
ok = cImageD11.mask_to_coo( self.target.astype(np.int8), i, j, tmp )
AttributeError: 'module' object has no attribute 'mask_to_coo'
======================================================================
ERROR: test_coo2 (test_clean_mask.test_clean_mask)
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_clean_mask.py", line 52, in test_coo2
ok = cImageD11.mask_to_coo( self.src.astype(np.int8), i, j, tmp )
AttributeError: 'module' object has no attribute 'mask_to_coo'
----------------------------------------------------------------------
Ran 3 tests in 0.002s
FAILED (errors=3)
Running suite for test_closest_vec
E
======================================================================
ERROR: test_same_as_python (test_closest_vec.test_closest_vec)
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_closest_vec.py", line 28, in test_same_as_python
cImageD11.closest_vec( self.data, r2 )
AttributeError: 'module' object has no attribute 'closest_vec'
----------------------------------------------------------------------
Ran 1 test in 1.081s
FAILED (errors=1)
Running suite for test_score_gvec_z
E
======================================================================
ERROR: test_same_as_python (test_score_gvec_z.test_closest_vec)
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_score_gvec_z.py", line 78, in test_same_as_python
cImageD11.score_gvec_z( UBI, UB, GVE,
AttributeError: 'module' object has no attribute 'score_gvec_z'
----------------------------------------------------------------------
Ran 1 test in 0.031s
FAILED (errors=1)
Running suite for test_sym_u
...........F
======================================================================
FAIL: test_trigonal (test_sym_u.testsyms)
----------------------------------------------------------------------
Traceback (most recent call last):
File "./test_sym_u.py", line 22, in test_trigonal
assert len(c.group) == 6
AssertionError
----------------------------------------------------------------------
Ran 12 tests in 2.387s
FAILED (failures=1)
Running suite for testcol
gv_general from /usr/local/lib/python2.7/dist-packages/ImageD11-1.9.0b0-py2.7-linux-mips64.egg/ImageD11/gv_general.pyc
....
----------------------------------------------------------------------
Ran 4 tests in 0.019s
OK
Running suite for test_misori
Error importing test_misori
Current folder is /home/junyue/Documents/xrd/ImageD11/test
Try removing .pyc files or __pycache__ folder if there is one
---RAISING----
Traceback (most recent call last):
File "run_tests.py", line 56, in <module>
MOD = importlib.import_module(M)
File "/usr/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
File "./test_misori.py", line 3, in <module>
from ImageD11.cImageD11 import misori_cubic, misori_cubic_pairs, \
ImportError: cannot import name misori_cubic
But I can run ImageD11_gui.py, version is 1.9.7 I tried load some filtered peaks by PolyXSim, so far 'plot tth/eta' works good.
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jonwright
commented on September 24, 2024
Sounds like it didn't compile the c codes yet? It might work it you try again. Otherwise, can you send the output of python setup.py build to try to track down the problem? Thanks!
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junyuewang
commented on September 24, 2024
It is done just in one minute, some output:
changing mode of build/bdist.linux-mips64/wheel/ImageD11-1.9.7.data/scripts/peaksearch.py to 755
running install_clib
customize UnixCCompiler
adding license file "LICENSE" (matched pattern "LICEN[CS]E*")
creating build/bdist.linux-mips64/wheel/ImageD11-1.9.7.dist-info/WHEEL
creating '/tmp/pip-wheel-vv5ljoww/ImageD11-1.9.7-cp37-cp37m-linux_mips64.whl' and adding 'build/bdist.linux-mips64/wheel' to it
adding 'ImageD11/ImageD11_file_series.py'
adding 'ImageD11/ImageD11_thread.py'
adding 'ImageD11/ImageD11options.py'
adding 'ImageD11/__init__.py'
adding 'ImageD11/blobcorrector.py'
adding 'ImageD11/cImageD11.py'
adding 'ImageD11/cImageD11_docstrings.py'
adding 'ImageD11/cImageD11_fast.cpython-37m-mips64el-linux-gnuabi64.so'
adding 'ImageD11/cImageD11_safe.cpython-37m-mips64el-linux-gnuabi64.so'
adding 'ImageD11/columnfile.py'
adding 'ImageD11/compute_fazit.py'
adding 'ImageD11/correct.py'
adding 'ImageD11/eps_sig_solver.py'
adding 'ImageD11/fft_index_refac.py'
adding 'ImageD11/finite_strain.py'
adding 'ImageD11/grain.py'
adding 'ImageD11/grid_index_parallel.py'
adding 'ImageD11/guicommand.py'
adding 'ImageD11/gv_general.py'
adding 'ImageD11/indexer.py'
adding 'ImageD11/indexing.py'
adding 'ImageD11/labelimage.py'
adding 'ImageD11/lattice_reduction.py'
adding 'ImageD11/license.py'
adding 'ImageD11/parameters.py'
adding 'ImageD11/peakmerge.py'
adding 'ImageD11/peaksearcher.py'
adding 'ImageD11/rc_array.py'
adding 'ImageD11/refinegrains.py'
adding 'ImageD11/rotdex.py'
adding 'ImageD11/rsv.py'
adding 'ImageD11/rsv_mapper.py'
adding 'ImageD11/saintraw.py'
adding 'ImageD11/scale.py'
adding 'ImageD11/simplex.py'
adding 'ImageD11/sparseframe.py'
adding 'ImageD11/sym_u.py'
adding 'ImageD11/symops.py'
adding 'ImageD11/threshold_image.py'
adding 'ImageD11/transform.py'
adding 'ImageD11/transformer.py'
adding 'ImageD11/unitcell.py'
adding 'ImageD11/write_graindex_gv.py'
adding 'ImageD11/silxGui/__init__.py'
adding 'ImageD11/silxGui/silx_colfile.py'
adding 'ImageD11/silxGui/silx_plot3d.py'
adding 'ImageD11/silxGui/silx_sptview.py'
adding 'ImageD11/tkGui/__init__.py'
adding 'ImageD11/tkGui/guiindexer.py'
adding 'ImageD11/tkGui/guimaker.py'
adding 'ImageD11/tkGui/guipeaksearch.py'
adding 'ImageD11/tkGui/guisolver.py'
adding 'ImageD11/tkGui/guitransformer.py'
adding 'ImageD11/tkGui/listdialog.py'
adding 'ImageD11/tkGui/plot3d.py'
adding 'ImageD11/tkGui/twodplot.py'
adding 'ImageD11-1.9.7.data/scripts/ImageD11_2_shelx.py'
adding 'ImageD11-1.9.7.data/scripts/ImageD11_gui.py'
adding 'ImageD11-1.9.7.data/scripts/avg_par.py'
adding 'ImageD11-1.9.7.data/scripts/bgmaker.py'
adding 'ImageD11-1.9.7.data/scripts/cutgrains.py'
adding 'ImageD11-1.9.7.data/scripts/edfheader.py'
adding 'ImageD11-1.9.7.data/scripts/filtergrain.py'
adding 'ImageD11-1.9.7.data/scripts/fit2dcake.py'
adding 'ImageD11-1.9.7.data/scripts/fitgrain.py'
adding 'ImageD11-1.9.7.data/scripts/fix_spline.py'
adding 'ImageD11-1.9.7.data/scripts/huber2bruker.py'
adding 'ImageD11-1.9.7.data/scripts/id11_summarize.py'
adding 'ImageD11-1.9.7.data/scripts/index_unknown.py'
adding 'ImageD11-1.9.7.data/scripts/makemap.py'
adding 'ImageD11-1.9.7.data/scripts/merge_flt.py'
adding 'ImageD11-1.9.7.data/scripts/pars_2_sweeper.py'
adding 'ImageD11-1.9.7.data/scripts/peaksearch.py'
adding 'ImageD11-1.9.7.data/scripts/plot3d.py'
adding 'ImageD11-1.9.7.data/scripts/plotImageD11map.py'
adding 'ImageD11-1.9.7.data/scripts/plotedf.py'
adding 'ImageD11-1.9.7.data/scripts/plotgrainhist.py'
adding 'ImageD11-1.9.7.data/scripts/plotlayer.py'
adding 'ImageD11-1.9.7.data/scripts/powderimagetopeaks.py'
adding 'ImageD11-1.9.7.data/scripts/refine_em.py'
adding 'ImageD11-1.9.7.data/scripts/rsv_mapper.py'
adding 'ImageD11-1.9.7.data/scripts/rubber.py'
adding 'ImageD11-1.9.7.data/scripts/spatialfix.py'
adding 'ImageD11-1.9.7.data/scripts/tomapper.py'
adding 'ImageD11-1.9.7.data/scripts/ubi2cellpars.py'
adding 'ImageD11-1.9.7.dist-info/LICENSE'
adding 'ImageD11-1.9.7.dist-info/METADATA'
adding 'ImageD11-1.9.7.dist-info/WHEEL'
adding 'ImageD11-1.9.7.dist-info/top_level.txt'
adding 'ImageD11-1.9.7.dist-info/RECORD'
removing build/bdist.linux-mips64/wheel
done
Stored in directory: /tmp/pip-ephem-wheel-cache-rbcr2r3b/wheels/1f/40/96/e2b99858642942d3db3ac113be696cb27933af066b812611fb
Removing source in /tmp/pip-req-build-l7tcmmwx
Successfully built ImageD11
Cleaning up...
Removed build tracker '/tmp/pip-req-tracker-7sulcc47'
but at beginning:
python3 -m pip -v install git+https://github.com/FABLE-3DXRD/ImageD11.git
Created temporary directory: /tmp/pip-ephem-wheel-cache-rbcr2r3b
Created temporary directory: /tmp/pip-req-tracker-7sulcc47
Created requirements tracker '/tmp/pip-req-tracker-7sulcc47'
Created temporary directory: /tmp/pip-install-06e7tgyq
Collecting git+https://github.com/FABLE-3DXRD/ImageD11.git
Created temporary directory: /tmp/pip-req-build-l7tcmmwx
Cloning https://github.com/FABLE-3DXRD/ImageD11.git to /tmp/pip-req-build-l7tcmmwx
Running command git clone -q https://github.com/FABLE-3DXRD/ImageD11.git /tmp/pip-req-build-l7tcmmwx
Added git+https://github.com/FABLE-3DXRD/ImageD11.git to build tracker '/tmp/pip-req-tracker-7sulcc47'
Running setup.py (path:/tmp/pip-req-build-l7tcmmwx/setup.py) egg_info for package from git+https://github.com/FABLE-3DXRD/ImageD11.git
Running command python setup.py egg_info
cc: error: unrecognized command line option ‘-mcpu=native’; did you mean ‘-march=native’?
Fast args are ['-mtune=native', '-march=native']
Building version |1.9.7|
Call create_cpu_check
Call bldlib
Seems to build OK
running egg_info
running build_src
build_src
building extension "cImageD11_safe" sources
creating build
creating build/src.linux-mips64-3.7
creating build/src.linux-mips64-3.7/src
f2py options: []
f2py: src/cImageD11_safe.pyf
Reading fortran codes...
Reading file 'src/cImageD11_safe.pyf' (format:free)
Line #96 in src/cImageD11_safe.pyf:" intent(c) "
All arguments will have attribute intent(c)
Line #117 in src/cImageD11_safe.pyf:" intent(c) "
All arguments will have attribute intent(c)
and for python setup.py build, similar error at beginning:
python setup.py build
cc: error: unrecognized command line option ‘-mcpu=native’; did you mean ‘-march=native’?
('Fast args are', ['-mtune=native', '-march=native'])
Building version |1.9.7|
Call create_cpu_check
Call bldlib
Seems to build OK
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building extension "cImageD11_safe" sources
f2py options: []
f2py: src/cImageD11_safe.pyf
Reading fortran codes...
Reading file 'src/cImageD11_safe.pyf' (format:free)
Line #96 in src/cImageD11_safe.pyf:" intent(c) "
All arguments will have attribute intent(c)
last few lines of output:
build/src.linux-mips64-2.7/src/cImageD11_fastmodule.c:157:12: warning: ‘f2py_size’ defined but not used [-Wunused-function]
static int f2py_size(PyArrayObject* var, ...)
^~~~~~~~~
mips64el-linux-gnuabi64-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-LcFEUM/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-LcFEUM/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-mips64-2.7/build/src.linux-mips64-2.7/src/cImageD11_fastmodule.o build/temp.linux-mips64-2.7/build/src.linux-mips64-2.7/build/src.linux-mips64-2.7/src/fortranobject.o -L./src -lcImageD11_Linux_64bit_mips64_2.7_fast -o build/lib.linux-mips64-2.7/ImageD11/cImageD11_fast.so -O2 -fopenmp -fPIC -std=c99 -DF2PY_REPORT_ON_ARRAY_COPY=1.
running build_scripts
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jonwright
commented on September 24, 2024
Thanks for digging into this. I don't see what is wrong here? The "cc: error" at the beginning is the script figuring out that it cannot use -march=native and then it goes on to say "seems to build OK".
Can you check the output from this:
python -v -c 'import ImageD11.cImageD11' 2>&1 | grep ImageD11
Thanks!
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junyuewang
commented on September 24, 2024
python -v -c 'import ImageD11.cImageD11' 2>&1 | grep ImageD11
import ImageD11 # directory /usr/local/lib/python2.7/dist-packages/ImageD11-1.9.0b0-py2.7-linux-mips64.egg/ImageD11
# /usr/local/lib/python2.7/dist-packages/ImageD11-1.9.0b0-py2.7-linux-mips64.egg/ImageD11/__init__.pyc matches /usr/local/lib/python2.7/dist-packages/ImageD11-1.9.0b0-py2.7-linux-mips64.egg/ImageD11/__init__.py
import ImageD11 # precompiled from /usr/local/lib/python2.7/dist-packages/ImageD11-1.9.0b0-py2.7-linux-mips64.egg/ImageD11/__init__.pyc
dlopen("/usr/local/lib/python2.7/dist-packages/ImageD11-1.9.0b0-py2.7-linux-mips64.egg/ImageD11/cImageD11.so", 2);
import ImageD11.cImageD11 # dynamically loaded from /usr/local/lib/python2.7/dist-packages/ImageD11-1.9.0b0-py2.7-linux-mips64.egg/ImageD11/cImageD11.so
# cleanup[1] ImageD11
# cleanup[1] ImageD11.cImageD11
looks like everything works great
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jonwright
commented on September 24, 2024
Looks like you are getting an old version 1.9.0 ? From git it should be 1.9.7. This would explain the tests failing. But if it works then perhaps it doesn't matter for now? Before uploading a new one it would be good to fix it. In principle you should be able to use python 3 (except for FitAllB). Something like a -U --no-deps on the end of pip install might help.
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junyuewang
commented on September 24, 2024
I installed 1.9.0 just before reporting. Now pip installed 1.9.7. When I type ImageD11_gui.py, 1.9.7 actually comes out. Something messed up here. Since it works it does not matter. Will try next time on a new machine. Many thanks again!
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jonwright
commented on September 24, 2024
I assume this is fixed - just needs a new release
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Related Issues (20)
- mlem output_size fails for even output size
- Concurrent Futures style multiprocessing context manager
- Sinogram class HOT 2
- Peakselect module HOT 2
- Make sandbox importable
- Grain recon class HOT 2
- mask argument for mlem is not used internally HOT 5
- Get rid of the shared memory arrays : add a colfile mmap option HOT 2
- sinograms.geometry module HOT 2
- Module based spatial distortions HOT 1
- GrainMap class HOT 3
- notebooks are not in the install HOT 1
- makemap.py introduces a rotation to grain positions in the lab frame for hexagonal systems HOT 1
- Left handed grains from index_unknown
- `ImageD11.columnfile.columnfile` fails to synchronize across `__setattr__` and `__getitem__` calls HOT 5
- Allow no mask to be used with lima_segmenter
- Default values with update_path() in dataset.py HOT 5
- PBP Code seems flipped in horizontal axis HOT 1
- get_ring_current_per_scan does not work for fscan2d data HOT 1
- Saving processing parameters & Nexus output, etc HOT 11
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