diff options
| -rw-r--r-- | .gitignore | 66 | ||||
| -rwxr-xr-x | Wrappers/Python/ccpi/framework/framework.py | 41 | ||||
| -rw-r--r-- | Wrappers/Python/test/test_subset.py | 141 |
3 files changed, 234 insertions, 14 deletions
diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..acac237 --- /dev/null +++ b/.gitignore @@ -0,0 +1,66 @@ +# ========================= +# Operating System Files +# ========================= + +# OSX +# ========================= + +.DS_Store +.AppleDouble +.LSOverride + +# Thumbnails +._* + +# Files that might appear on external disk +.Spotlight-V100 +.Trashes + +# Directories potentially created on remote AFP share +.AppleDB +.AppleDesktop +Network Trash Folder +Temporary Items +.apdisk + +# Windows +# ========================= + +# Windows image file caches +Thumbs.db +ehthumbs.db + +# Folder config file +Desktop.ini + +# Recycle Bin used on file shares +$RECYCLE.BIN/ + +# Windows Installer files +*.cab +*.msi +*.msm +*.msp + +# Windows shortcuts +*.lnk + +# User-specific files +*.o +*.a +*.dll +*.so +*.h5 +*.pyd +*.pyc +*.tmp +*.nxs + +# Common editor backups +~$* +*~ +*.bak +\#* +.#* + + diff --git a/Wrappers/Python/ccpi/framework/framework.py b/Wrappers/Python/ccpi/framework/framework.py index 627e6d2..c30c436 100755 --- a/Wrappers/Python/ccpi/framework/framework.py +++ b/Wrappers/Python/ccpi/framework/framework.py @@ -110,6 +110,8 @@ class ImageGeometry(object): if order != [i for i in range(len(dim_labels))]: # resort self.shape = tuple([shape[i] for i in order]) + else: + self.shape = tuple(order) self.dimension_labels = labels def get_order_by_label(self, dimension_labels, default_dimension_labels): @@ -316,12 +318,12 @@ class AcquisitionGeometry(object): if not reduce(lambda x,y: (y in allowed_labels) and x, labels , True): raise ValueError('Requested axis are not possible. Expected {},\ngot {}'.format( allowed_labels,labels)) - if len(labels) != len(dim_labels): - raise ValueError('Wrong number of labels. Expected {} got {}'.format(len(dim_labels), len(labels))) order = self.get_order_by_label(labels, dim_labels) if order != [i for i in range(len(dim_labels))]: # resort self.shape = tuple([shape[i] for i in order]) + else: + self.shape = tuple(order) self.dimension_labels = labels def get_order_by_label(self, dimension_labels, default_dimension_labels): @@ -447,7 +449,6 @@ class DataContainer(object): raise ValueError('Unknown dimension {0}. Should be one of'.format(dimension_label, self.dimension_labels.values())) - def as_array(self, dimensions=None): '''Returns the DataContainer as Numpy Array @@ -1199,20 +1200,24 @@ class AcquisitionData(DataContainer): def subset(self, dimensions=None, **kw): '''returns a subset of the AcquisitionData and regenerates the geometry''' + # # Check that this is actually a resorting + # if dimensions is not None and \ + # (len(dimensions) != len(self.shape) ): + # raise ValueError('Please specify the slice on the axis/axes you want to cut away, or the same amount of axes for resorting') + + # requested_labels = kw.get('dimension_labels', None) + # if requested_labels is not None: + # allowed_labels = [AcquisitionGeometry.CHANNEL, + # AcquisitionGeometry.ANGLE, + # AcquisitionGeometry.VERTICAL, + # AcquisitionGeometry.HORIZONTAL] + # if not reduce(lambda x,y: (y in allowed_labels) and x, requested_labels , True): + # raise ValueError('Requested axis are not possible. Expected {},\ngot {}'.format( + # allowed_labels,requested_labels)) # Check that this is actually a resorting if dimensions is not None and \ (len(dimensions) != len(self.shape) ): raise ValueError('Please specify the slice on the axis/axes you want to cut away, or the same amount of axes for resorting') - - requested_labels = kw.get('dimension_labels', None) - if requested_labels is not None: - allowed_labels = [AcquisitionGeometry.CHANNEL, - AcquisitionGeometry.ANGLE, - AcquisitionGeometry.VERTICAL, - AcquisitionGeometry.HORIZONTAL] - if not reduce(lambda x,y: (y in allowed_labels) and x, requested_labels , True): - raise ValueError('Requested axis are not possible. Expected {},\ngot {}'.format( - allowed_labels,requested_labels)) out = super(AcquisitionData, self).subset(dimensions, **kw) if out.number_of_dimensions > 1: @@ -1226,6 +1231,14 @@ class AcquisitionData(DataContainer): pixel_size_v = 1 dist_source_center = self.geometry.dist_source_center dist_center_detector = self.geometry.dist_center_detector + + # update the angles if necessary + sliceme = kw.get(AcquisitionGeometry.ANGLE, None) + if sliceme is not None: + angles = numpy.asarray([ self.geometry.angles[sliceme] ] , numpy.float32) + else: + angles = self.geometry.angles.copy() + for key in out.dimension_labels.keys(): if out.dimension_labels[key] == AcquisitionGeometry.CHANNEL: channels = self.geometry.channels @@ -1243,7 +1256,7 @@ class AcquisitionData(DataContainer): out.geometry = AcquisitionGeometry(geom_type=self.geometry.geom_type, dimension=dim, - angles=self.geometry.angles, + angles=angles, pixel_num_h=pixel_num_h, pixel_size_h = pixel_size_h, pixel_num_v = pixel_num_v, diff --git a/Wrappers/Python/test/test_subset.py b/Wrappers/Python/test/test_subset.py new file mode 100644 index 0000000..dd017fb --- /dev/null +++ b/Wrappers/Python/test/test_subset.py @@ -0,0 +1,141 @@ +# -*- coding: utf-8 -*- +# CCP in Tomographic Imaging (CCPi) Core Imaging Library (CIL). + +# Copyright 2017 UKRI-STFC +# Copyright 2017 University of Manchester + +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at + +# http://www.apache.org/licenses/LICENSE-2.0 + +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +import sys +import unittest +import numpy +from ccpi.framework import DataContainer +from ccpi.framework import ImageData +from ccpi.framework import AcquisitionData +from ccpi.framework import ImageGeometry +from ccpi.framework import AcquisitionGeometry +from timeit import default_timer as timer + +class TestSubset(unittest.TestCase): + def setUp(self): + self.ig = ImageGeometry(1,2,3,channels=4) + angles = numpy.asarray([90.,0.,-90.], dtype=numpy.float32) + + self.ag = AcquisitionGeometry('cone', 'edo', pixel_num_h=20, pixel_num_v=2, angles=angles, + dist_source_center = 312.2, + dist_center_detector = 123., + channels=4 ) + + def test_ImageDataAllocate1a(self): + data = self.ig.allocate() + default_dimension_labels = [ImageGeometry.CHANNEL, ImageGeometry.VERTICAL, + ImageGeometry.HORIZONTAL_Y, ImageGeometry.HORIZONTAL_X] + self.assertTrue( default_dimension_labels == list(data.dimension_labels.values()) ) + def test_ImageDataAllocate1b(self): + data = self.ig.allocate() + default_dimension_labels = [ImageGeometry.CHANNEL, ImageGeometry.VERTICAL, + ImageGeometry.HORIZONTAL_Y, ImageGeometry.HORIZONTAL_X] + self.assertTrue( data.shape == (4,3,2,1)) + + def test_ImageDataAllocate2a(self): + non_default_dimension_labels = [ ImageGeometry.HORIZONTAL_X, ImageGeometry.VERTICAL, + ImageGeometry.HORIZONTAL_Y, ImageGeometry.CHANNEL] + data = self.ig.allocate(dimension_labels=non_default_dimension_labels) + self.assertTrue( non_default_dimension_labels == list(data.dimension_labels.values()) ) + + def test_ImageDataAllocate2b(self): + non_default_dimension_labels = [ ImageGeometry.HORIZONTAL_X, ImageGeometry.VERTICAL, + ImageGeometry.HORIZONTAL_Y, ImageGeometry.CHANNEL] + data = self.ig.allocate(dimension_labels=non_default_dimension_labels) + self.assertTrue( data.shape == (1,3,2,4)) + + def test_AcquisitionDataAllocate1a(self): + data = self.ag.allocate() + default_dimension_labels = [AcquisitionGeometry.CHANNEL , + AcquisitionGeometry.ANGLE , AcquisitionGeometry.VERTICAL , + AcquisitionGeometry.HORIZONTAL] + self.assertTrue( default_dimension_labels == list(data.dimension_labels.values()) ) + + def test_AcquisitionDataAllocate1b(self): + data = self.ag.allocate() + default_dimension_labels = [AcquisitionGeometry.CHANNEL , + AcquisitionGeometry.ANGLE , AcquisitionGeometry.VERTICAL , + AcquisitionGeometry.HORIZONTAL] + + self.assertTrue( data.shape == (4,3,2,20)) + + def test_AcquisitionDataAllocate2a(self): + non_default_dimension_labels = [AcquisitionGeometry.CHANNEL, AcquisitionGeometry.HORIZONTAL, + AcquisitionGeometry.VERTICAL, AcquisitionGeometry.ANGLE] + data = self.ag.allocate(dimension_labels=non_default_dimension_labels) + + + self.assertTrue( non_default_dimension_labels == list(data.dimension_labels.values()) ) + + def test_AcquisitionDataAllocate2b(self): + non_default_dimension_labels = [AcquisitionGeometry.CHANNEL, AcquisitionGeometry.HORIZONTAL, + AcquisitionGeometry.VERTICAL, AcquisitionGeometry.ANGLE] + data = self.ag.allocate(dimension_labels=non_default_dimension_labels) + self.assertTrue( data.shape == (4,20,2,3)) + + def test_AcquisitionDataSubset1a(self): + non_default_dimension_labels = [AcquisitionGeometry.CHANNEL, AcquisitionGeometry.HORIZONTAL, + AcquisitionGeometry.VERTICAL, AcquisitionGeometry.ANGLE] + data = self.ag.allocate(dimension_labels=non_default_dimension_labels) + #self.assertTrue( data.shape == (4,20,2,3)) + sub = data.subset(vertical = 0) + self.assertTrue( sub.shape == (4,20,3)) + + def test_AcquisitionDataSubset1b(self): + non_default_dimension_labels = [AcquisitionGeometry.CHANNEL, AcquisitionGeometry.HORIZONTAL, + AcquisitionGeometry.VERTICAL, AcquisitionGeometry.ANGLE] + data = self.ag.allocate(dimension_labels=non_default_dimension_labels) + #self.assertTrue( data.shape == (4,20,2,3)) + sub = data.subset(channel = 0) + self.assertTrue( sub.shape == (20,2,3)) + def test_AcquisitionDataSubset1c(self): + non_default_dimension_labels = [AcquisitionGeometry.CHANNEL, AcquisitionGeometry.HORIZONTAL, + AcquisitionGeometry.VERTICAL, AcquisitionGeometry.ANGLE] + data = self.ag.allocate(dimension_labels=non_default_dimension_labels) + #self.assertTrue( data.shape == (4,20,2,3)) + sub = data.subset(horizontal = 0) + self.assertTrue( sub.shape == (4,2,3)) + def test_AcquisitionDataSubset1d(self): + non_default_dimension_labels = [AcquisitionGeometry.CHANNEL, AcquisitionGeometry.HORIZONTAL, + AcquisitionGeometry.VERTICAL, AcquisitionGeometry.ANGLE] + data = self.ag.allocate(dimension_labels=non_default_dimension_labels) + #self.assertTrue( data.shape == (4,20,2,3)) + sliceme = 1 + sub = data.subset(angle = sliceme) + #print (sub.shape , sub.dimension_labels) + self.assertTrue( sub.shape == (4,20,2) ) + self.assertTrue( sub.geometry.angles[0] == data.geometry.angles[sliceme]) + def test_AcquisitionDataSubset1e(self): + non_default_dimension_labels = [AcquisitionGeometry.CHANNEL, AcquisitionGeometry.HORIZONTAL, + AcquisitionGeometry.VERTICAL, AcquisitionGeometry.ANGLE] + data = self.ag.allocate(dimension_labels=non_default_dimension_labels) + #self.assertTrue( data.shape == (4,20,2,3)) + sliceme = 1 + sub = data.subset(angle = sliceme) + self.assertTrue( sub.geometry.angles[0] == data.geometry.angles[sliceme]) + def test_AcquisitionDataSubset1f(self): + + data = self.ag.allocate() + #self.assertTrue( data.shape == (4,20,2,3)) + sliceme = 1 + sub = data.subset(angle = sliceme) + self.assertTrue( sub.geometry.angles[0] == data.geometry.angles[sliceme]) + + + + +
\ No newline at end of file |