marinerhemant / midas

The repository provides codes under the Microstructural Identification using Diffraction Analysis Software

MIDAS

**** V5 Released ****

Code for reduction of Near-Field and Far-Field High Energy Diffraction Microscopy (HEDM) data developed at Advanced Photon Source.

In case of problems, contatct Hemant Sharma.

SGInfo library used to calculate HKLs.

Some misorientation functions are taken from the ODFPF package from Cornell.

Downloads JRE, SWIFT, NLOPT, LIBTIFF, FFTW, HDF5, MPICH, ZLIB for compilation of N(F)F-HEDM codes.

More details at MIDAS-WIKI

midas's Issues

Linked list all matched NF

Implement a sorted linked list for NF all matches

Documentation: clarifications of inputs for MatchGrains script

Hi,

It would be useful to add further documentation of the input parameters for the MatchGrains script, including

stateN.txt:

• A file containing a list of Grains.csv files or a Grains.csv file directly.
• If a list of Grains.csv files is provided, the results will be merged into a single file.

SGnr:

• Space group number (e.g., 225 for most common FCC systems)

Also, in what scenario would the user provide an input for referenceMisorientation? This could use an explanation similar to the one provided for the two options of removeDuplicates.

Best regards,
Kris

Krzysztof Stopka

matchGrains FF

Check if remove duplicates 1 needs greater number of grains for state1 or state2 in MatchGrains

Fix swift conf for Edison

We need the ip of each login node to run this.

Strains Kenesei

Instead of g_distorted, use g_undistorted to fit.

Indexer with mixed friedel pairs

Still to implement.

Twins volumes to be fixed

Check for non overlapping volumes and use those.

AutoCalibrate.py script expects user to execute command in same directory as the DATAFN and DARKFN.

Hi Hemant,

I am logging this bug based on our conservation:

The AutoCalibrate.py script takes as input the path to the Ceria scan and the dark file. When I ran this, the “CeO2_3s_100x100_att000_840mm_71p68keV_000412.edf.ge5.corr.csv” file was generated in the same directory where I ran the .sh script that calls this function, which was different than where I have my data and dark files. I got the error below because the script expects that the user will always execute the script/command to AutoCalibrate.py in the same directory as the DATAFN and DARKFN.

AutoCalibrate.py fails on line 134. This can be fixed if line 1453 in CalibrantOMP.c considers the directory where the script is executed.

Running MIDAS calibration, might take a few minutes.     Trial Nr: 1
Path of int:
/scratch/negishi/kstopka/sangid_sep22/ge5/CeO2_3s_100x100_att000_840mm_71p68keV_000412.edf.ge5
Traceback (most recent call last):
  File "/home/kstopka/opt/MIDAS/utils/AutoCalibrate.py", line 314, in <module>
    rOrig = runMIDAS(rawFN)
            ^^^^^^^^^^^^^^^
  File "/home/kstopka/opt/MIDAS/utils/AutoCalibrate.py", line 134, in runMIDAS
    results = np.genfromtxt(fn+'.corr.csv',skip_header=1)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/apps/spack/negishi/apps/anaconda/2024.02-py311-gcc-8.5.0-lr57z2f/lib/python3.11/site-packages/numpy/lib/npyio.py", line 1980, in genfromtxt
    fid = np.lib._datasource.open(fname, 'rt', encoding=encoding)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/apps/spack/negishi/apps/anaconda/2024.02-py311-gcc-8.5.0-lr57z2f/lib/python3.11/site-packages/numpy/lib/_datasource.py", line 193, in open
    return ds.open(path, mode, encoding=encoding, newline=newline)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/apps/spack/negishi/apps/anaconda/2024.02-py311-gcc-8.5.0-lr57z2f/lib/python3.11/site-packages/numpy/lib/_datasource.py", line 533, in open
    raise FileNotFoundError(f"{path} not found.")
FileNotFoundError: /scratch/negishi/kstopka/sangid_sep22/ge5/CeO2_3s_100x100_att000_840mm_71p68keV_000412.edf.ge5.corr.csv not found.

Best regards,
Krzysztof Stopka