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Small fixes/enhancement to ALS readers #25

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merged 9 commits into from
May 12, 2016
Merged

Small fixes/enhancement to ALS readers #25

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df6b8c2
ALS h5 reader returns only 3 values unless multiple flat fields flag …
lbluque May 5, 2016
c5d4c62
Added proj and sino slice keywords to als reader
lbluque May 5, 2016
62b4c88
Included context manager for h5py objects in als hdf5 reader.
lbluque May 5, 2016
666fae9
forgot to actually put h5py object in context manager. Done now.
lbluque May 5, 2016
5f153f5
Added sino slicing to als tiff reader
May 5, 2016
675bac4
Added sino slicing to als tiff reader
May 5, 2016
82f0648
Added sino slicing to als tiff reader
May 5, 2016
6760a01
Merge branch 'master' of https://github.com/data-exchange/dxchange
May 5, 2016
468f034
removed variable return values from als reader
May 7, 2016
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -110,6 +110,7 @@ coverage.xml
*.sublime-workspace
docs/trunk/*
.spyder*
.idea

# Francesco's #
################
Expand Down
103 changes: 52 additions & 51 deletions dxchange/exchange.py
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Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,7 @@
logger = logging.getLogger(__name__)


def read_als_832(fname, ind_tomo=None, normalized=False):
def read_als_832(fname, ind_tomo=None, normalized=False, sino=None):
"""
Read ALS 8.3.2 standard data format.

Expand All @@ -104,6 +104,9 @@ def read_als_832(fname, ind_tomo=None, normalized=False):
8.3.2 has a plugin that normalization is preferred to be
done with prior to tomopy reconstruction.

sino : {sequence, int}, optional
Specify sinograms to read. (start, end, step)

Returns
-------
ndarray
Expand All @@ -120,8 +123,6 @@ def read_als_832(fname, ind_tomo=None, normalized=False):
fname = os.path.abspath(fname)

if not normalized:
fname = fname.split(
'output')[0] + fname.split('/')[len(fname.split('/')) - 1]
tomo_name = fname + '_0000_0000.tif'
flat_name = fname + 'bak_0000.tif'
dark_name = fname + 'drk_0000.tif'
Expand Down Expand Up @@ -157,7 +158,8 @@ def read_als_832(fname, ind_tomo=None, normalized=False):
ind_dark = list(range(0, ndark))

# Read image data from tiff stack.
tomo = dxreader.read_tiff_stack(tomo_name, ind=ind_tomo, digit=4)
tomo = dxreader.read_tiff_stack(tomo_name, ind=ind_tomo, digit=4,
slc=(sino, None))
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I do not know this code, but that sometime you are using (sino, None) and other time (None, sino) is a really bad code smell.

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@tacaswell it does smell bad ... thank you for point it out. For some reason we are flipping the order between datasets consisting of multiple files (tiff, xrm) vs single files (hdf, netcdf etc.). We should make it consistent.

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@dgursoy fix seems easy, just swap the loop indexing at

def _shape_after_slice(shape, slc):

but will make it not back compatible. Suggestions?


if not normalized:

Expand Down Expand Up @@ -190,9 +192,10 @@ def read_als_832(fname, ind_tomo=None, normalized=False):
dy, dz = _arr.shape
flat = np.zeros((dx, dy, dz))
flat[m] = _arr
flat = dxreader._slice_array(flat, None)
flat = dxreader._slice_array(flat, (None, sino))
else:
flat = dxreader.read_tiff_stack(flat_name, ind=ind_flat, digit=4)
flat = dxreader.read_tiff_stack(flat_name, ind=ind_flat, digit=4,
slc=(sino, None))

# Adheres to 8.3.2 flat/dark naming conventions:
# ----Darks----
Expand All @@ -215,7 +218,7 @@ def read_als_832(fname, ind_tomo=None, normalized=False):
dy, dz = _arr.shape
dark = np.zeros((dx, dy, dz))
dark[m] = _arr
dark = dxreader._slice_array(dark, None)
dark = dxreader._slice_array(dark, (None, sino))
else:
flat = np.ones(1)
dark = np.zeros(1)
Expand Down Expand Up @@ -263,63 +266,61 @@ def read_als_832h5(fname, ind_tomo=None, ind_flat=None, ind_dark=None,
Indices of flat field data within tomography projection list
"""

dgroup = dxreader.find_dataset_group(fname)
dname = dgroup.name.split('/')[-1]
with dxreader.find_dataset_group(fname) as dgroup:
dname = dgroup.name.split('/')[-1]

tomo_name = dname + '_0000_0000.tif'
flat_name = dname + 'bak_0000.tif'
dark_name = dname + 'drk_0000.tif'
tomo_name = dname + '_0000_0000.tif'
flat_name = dname + 'bak_0000.tif'
dark_name = dname + 'drk_0000.tif'

# Read metadata from dataset group attributes
keys = list(dgroup.attrs.keys())
if 'nangles' in keys:
nproj = int(dgroup.attrs['nangles'])
if 'i0cycle' in keys:
inter_bright = int(dgroup.attrs['i0cycle'])
if 'num_bright_field' in keys:
nflat = int(dgroup.attrs['num_bright_field'])
else:
nflat = dxreader._count_proj(dgroup, flat_name, nproj,
inter_bright=inter_bright)
if 'num_dark_fields' in keys:
ndark = int(dgroup.attrs['num_dark_fields'])
else:
ndark = dxreader._count_proj(dgroup, dark_name, nproj)
# Read metadata from dataset group attributes
keys = list(dgroup.attrs.keys())
if 'nangles' in keys:
nproj = int(dgroup.attrs['nangles'])
if 'i0cycle' in keys:
inter_bright = int(dgroup.attrs['i0cycle'])
if 'num_bright_field' in keys:
nflat = int(dgroup.attrs['num_bright_field'])
else:
nflat = dxreader._count_proj(dgroup, flat_name, nproj,
inter_bright=inter_bright)
if 'num_dark_fields' in keys:
ndark = int(dgroup.attrs['num_dark_fields'])
else:
ndark = dxreader._count_proj(dgroup, dark_name, nproj)

# Create arrays of indices to read projections, flats and darks
if ind_tomo is None:
ind_tomo = list(range(0, nproj))
ind_dark = list(range(0, ndark))
group_dark = [nproj - 1]
ind_flat = list(range(0, nflat))

if inter_bright > 0:
group_flat = list(range(0, nproj, inter_bright))
if group_flat[-1] != nproj - 1:
group_flat.append(nproj - 1)
elif inter_bright == 0:
group_flat = [0, nproj - 1]
else:
group_flat = None
# Create arrays of indices to read projections, flats and darks
if ind_tomo is None:
ind_tomo = list(range(0, nproj))
ind_dark = list(range(0, ndark))
group_dark = [nproj - 1]
ind_flat = list(range(0, nflat))

tomo = dxreader.read_hdf5_stack(
dgroup, tomo_name, ind_tomo, slc=(proj, sino))
if inter_bright > 0:
group_flat = list(range(0, nproj, inter_bright))
if group_flat[-1] != nproj - 1:
group_flat.append(nproj - 1)
elif inter_bright == 0:
group_flat = [0, nproj - 1]
else:
group_flat = None

flat = dxreader.read_hdf5_stack(dgroup, flat_name, ind_flat, slc=(None, sino),
out_ind=group_flat)
tomo = dxreader.read_hdf5_stack(
dgroup, tomo_name, ind_tomo, slc=(proj, sino))

dark = dxreader.read_hdf5_stack(dgroup, dark_name, ind_dark, slc=(None, sino),
out_ind=group_dark)
flat = dxreader.read_hdf5_stack(dgroup, flat_name, ind_flat, slc=(None, sino),
out_ind=group_flat)

group_flat = dxreader._map_loc(ind_tomo, group_flat)
dark = dxreader.read_hdf5_stack(dgroup, dark_name, ind_dark, slc=(None, sino),
out_ind=group_dark)

return tomo, flat, dark, group_flat
return tomo, flat, dark


def read_anka_topotomo(
fname, ind_tomo, ind_flat, ind_dark, proj=None, sino=None):
"""
Read ANKA TOMO-TOMO standard data format.
Read ANKA TOPO-TOMO standard data format.

Parameters
----------
Expand Down
6 changes: 4 additions & 2 deletions dxchange/reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -79,6 +79,7 @@
import re
import math
import struct
from contextlib import contextmanager
import dxchange.writer as writer
from dxchange.dtype import empty_shared_array

Expand Down Expand Up @@ -600,6 +601,7 @@ def _list_file_stack(fname, ind, digit):
list_fname.append(str(body + '{0:0={1}d}'.format(m, digit) + ext))
return list_fname

@contextmanager
def find_dataset_group(fname):
"""
Finds the group name containing the stack of projections datasets within
Expand All @@ -614,8 +616,8 @@ def find_dataset_group(fname):
-------
h5py.Group
"""
h5object = h5py.File(fname, 'r')
return _find_dataset_group(h5object)
with h5py.File(fname, 'r') as h5object:
yield _find_dataset_group(h5object)


def _find_dataset_group(h5object):
Expand Down