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4 add visualization functionality for morphology checker #7

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merged 10 commits into from
Oct 3, 2023
Merged

4 add visualization functionality for morphology checker #7

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1dc484d
Added visualizer as Morphology object function. Modified pybind tutorial
Feb 10, 2023
658ca96
remove axes deletion
pdudenas Feb 13, 2023
72c96c0
Additional tweaks and bugfixes to visualizer
Feb 21, 2023
5dd6b87
additional pugfixes for visualizer
Feb 21, 2023
beb353b
Cleanup of stub method following suggestions from @pbeaucage
Mar 9, 2023
dba6497
load_morph_hdf5 don't create cy object as default
pdudenas Mar 11, 2023
8074926
Adds quiver functionality and arguments for psi plots.
Mar 13, 2023
c13fb73
added warning if theta is outside bounds
Mar 13, 2023
850cb9d
tiny bugfix for warnings
Mar 13, 2023
22d1728
add plot export capability
BijalBPatel Sep 26, 2023
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Binary file added NRSS/cmap/infinitydouble_cmap.npy
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11 changes: 9 additions & 2 deletions NRSS/morphology.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,8 @@
from .checkH5 import check_NumMat
from .reader import read_material, read_config
from .writer import write_opts, write_hdf5
from .visualizer import morphology_visualizer

import numpy as np
import xarray as xr
import sys
Expand Down Expand Up @@ -287,7 +289,7 @@ def config(self, dict1):
warnings.warn(f'Key {key} not supported')

@classmethod
def load_morph_hdf5(cls, hdf5_file):
def load_morph_hdf5(cls, hdf5_file, create_cy_object=False):
with h5py.File(hdf5_file, 'r') as f:
if 'Euler_Angles' not in f.keys():
raise KeyError('Only the Euler Angle convention is currently supported')
Expand All @@ -309,7 +311,7 @@ def load_morph_hdf5(cls, hdf5_file):
psi=psi,
NumZYX=Vfrac.shape)

return cls(numMat, materials=materials, PhysSize=PhysSize)
return cls(numMat, materials=materials, PhysSize=PhysSize, create_cy_object=create_cy_object)

def load_config(self, config_file):
self.config = read_config(config_file)
Expand Down Expand Up @@ -487,6 +489,11 @@ def check_materials(self, quiet=True):
if not quiet:
print('All material checks have passed')

def visualize_materials(self, *args,**kwargs):
return morphology_visualizer(self, *args,**kwargs)
visualize_materials.__doc__ = morphology_visualizer.__doc__


def validate_all(self, quiet=True):
self.check_materials(quiet=quiet)
input_check = self.inputData.validate()
Expand Down
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