def test3(nodes):
ct = CT(
dir,
clean_intermediate_files=None,
vertical_range=slice(900, 1000),
parallel_nodes=nodes,
)
ct.recon(tilt=-1.40, explore_rot_center=False)
assert os.path.exists('work')
return
def test2(nodes):
ct = CT(dir,
clean_intermediate_files='archive',
vertical_range=slice(900, 1000),
parallel_nodes=nodes,
skip_df=True)
ct.recon(tilt=-1.40, explore_rot_center=False)
assert not os.path.exists('work')
import glob
assert glob.glob('out/work-*')
return
def test():
nodes = os.environ.get('NODES')
if nodes:
nodes = int(nodes)
print("Processing using %s nodes" % (nodes or 'all'))
from imars3d.CT import CT
ct = CT(
dir,
clean_on_the_fly=True,
vertical_range=slice(900, 1000),
parallel_nodes=nodes,
)
ct.recon(tilt=-1.40, explore_rot_center=False)
return
def nextStep(self):
"""
Creates and moves to the desired output directory.
Then, creates/opens that directory's recon-config.pkl file,
and dumps the contents of self.context.config into it.
Then, after printing the configuration, creates a ct object,
and stores the result in context.ct.
Finally, removes the current panel,
and replaces it with an MainUIPanel.
"""
# save path of current imars3d config
import imars3d
orig_imars3d_config = os.path.abspath(imars3d.conf_path)
# create output dir and move over there
os.makedirs(self.context.config.outdir)
os.chdir(self.context.config.outdir)
assert os.getcwd() == self.context.config.outdir
# copy imars3d config if it exists
if os.path.exists(orig_imars3d_config):
import shutil
shutil.copyfile(orig_imars3d_config, imars3d.conf_path)
# save recon config
with open('recon-config.pkl', 'wb') as open_config:
pkl.dump(self.context.config, open_config)
# logging
logger.info("Configuration:")
for k, v in self.context.config.__dict__.items():
if k.startswith('_'):
continue
sv = str(v)
if len(sv) > 60:
sv = sv[:50] + '...'
logger.info("{0:20}{1:<}".format(k, sv))
# create CT object
from imars3d.CT import CT
context = self.context
with wait_alert(
"Gathering information for the CT reconstruction. Please wait..."
):
ct = CT(context.config.datadir,
CT_subdir=context.config.ct_dir,
CT_identifier=context.config.ct_sig,
workdir=context.config.workdir,
outdir=context.config.outdir,
ob_files=context.config.ob_files,
df_files=context.config.df_files)
context.ct = ct
# new interface
self.remove()
imgslide = MainUIPanel(context)
imgslide.show()
def nextStep(self):
"""
Removes the current panel. Then, creates a ct object,
and saves it into context's ct member.
Fianlly, creates an MainUIPanel and displays it.
"""
self.remove()
from imars3d.CT import CT
context = self.context
ct = CT(context.config.datadir,
CT_subdir=context.config.ct_dir,
CT_identifier=context.config.ct_sig,
workdir=context.config.workdir,
outdir=context.config.outdir,
ob_files=context.config.ob_files,
df_files=context.config.df_files)
context.ct = ct
img_slide = MainUIPanel(context)
img_slide.show()
#!/usr/bin/env python
# -*- coding: utf-8 -*-
datadir = 'data'
workdir = "work"
outdir = "out"
import sys
import os, numpy as np, imars3d as i3, tomopy
from imars3d.CT import CT
ct = CT(datadir)
# dark field
dfs = i3.io.imageCollection(ct.DF_pattern, name="Dark Field")
# open beam
obs = i3.io.imageCollection(ct.OB_pattern, name="Open Beam")
# ct
angles = ct.angles
theta = angles * np.pi / 180.
pattern = ct.CT_pattern
ct_series = i3.io.ImageFileSeries(pattern, identifiers = angles, name = "CT")
def main():
normalized = i3.normalize(ct_series, dfs, obs, workdir=os.path.join(workdir, 'normalization'))
tilt_corrected = i3.correct_tilt(normalized, workdir=os.path.join(workdir, 'tilt-correction'))
if_corrected = i3.correct_intensity_fluctuation(tilt_corrected, workdir=os.path.join(workdir, 'intensity-fluctuation-correction'))
angles, sinograms = i3.build_sinograms(if_corrected, workdir=os.path.join(workdir, 'sinogram'))
# take the middle part to calculate the center of rotation
sino = [s.data for s in sinograms[900:1100]]
sino= np.array(sino)
proj = np.swapaxes(sino, 0, 1)
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
dir = os.path.dirname(__file__)
datadir = os.path.join(dir, "raw")
CT_subdir = os.path.join("ct_scans", "Derek_injec")
workdir = "work"
outdir = "out"
import sys
import numpy as np, imars3d as i3, tomopy
from imars3d.CT import CT
ct = CT(datadir, CT_subdir=CT_subdir, CT_identifier="Derek_injec")
# dark field
dfs = i3.io.imageCollection(ct.DF_pattern, name="Dark Field")
# open beam
obs = i3.io.imageCollection(ct.OB_pattern, name="Open Beam")
# ct
angles = ct.angles
theta = angles * np.pi / 180.
pattern = ct.CT_pattern
ct_series = i3.io.ImageFileSeries(pattern, identifiers=angles, name="CT")
def main():
normalized = i3.normalize(ct_series,
dfs,
obs,
workdir=os.path.join(workdir, 'normalization'))
def test():
from imars3d.CT import CT
ct = CT(dir)
ct.recon()
return