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-rwxr-xr-xWrappers/Python/ccpi/framework/Vector.py97
-rwxr-xr-xWrappers/Python/ccpi/framework/__init__.py2
-rwxr-xr-xWrappers/Python/ccpi/framework/framework.py222
-rw-r--r--Wrappers/Python/test/test_Operator.py4
4 files changed, 68 insertions, 257 deletions
diff --git a/Wrappers/Python/ccpi/framework/Vector.py b/Wrappers/Python/ccpi/framework/Vector.py
deleted file mode 100755
index 1885822..0000000
--- a/Wrappers/Python/ccpi/framework/Vector.py
+++ /dev/null
@@ -1,97 +0,0 @@
-# -*- 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.
-
-from __future__ import absolute_import
-from __future__ import division
-from __future__ import print_function
-from __future__ import unicode_literals
-
-import numpy
-import sys
-from datetime import timedelta, datetime
-import warnings
-from functools import reduce
-from numbers import Number
-from ccpi.framework import DataContainer
-
-class VectorData(DataContainer):
- '''DataContainer to contain 1D array'''
- def __init__(self, array=None, **kwargs):
- self.geometry = kwargs.get('geometry', None)
- self.dtype = kwargs.get('dtype', numpy.float32)
-
- if self.geometry is None:
- if array is None:
- raise ValueError('Please specify either a geometry or an array')
- else:
- if len(array.shape) > 1:
- raise ValueError('Incompatible size: expected 1D got {}'.format(array.shape))
- out = array
- self.geometry = VectorGeometry(array.shape[0])
- self.length = self.geometry.length
- else:
- self.length = self.geometry.length
-
- if array is None:
- out = numpy.zeros((self.length,), dtype=self.dtype)
- else:
- if self.length == array.shape[0]:
- out = array
- else:
- raise ValueError('Incompatible size: expecting {} got {}'.format((self.length,), array.shape))
- deep_copy = True
- super(VectorData, self).__init__(out, deep_copy, None)
-
-class VectorGeometry(object):
- '''Geometry describing VectorData to contain 1D array'''
- RANDOM = 'random'
- RANDOM_INT = 'random_int'
-
- def __init__(self,
- length):
-
- self.length = length
- self.shape = (length, )
-
-
- def clone(self):
- '''returns a copy of VectorGeometry'''
- return VectorGeometry(self.length)
-
- def allocate(self, value=0, **kwargs):
- '''allocates an VectorData according to the size expressed in the instance'''
- self.dtype = kwargs.get('dtype', numpy.float32)
- out = VectorData(geometry=self, dtype=self.dtype)
- if isinstance(value, Number):
- if value != 0:
- out += value
- else:
- if value == VectorGeometry.RANDOM:
- seed = kwargs.get('seed', None)
- if seed is not None:
- numpy.random.seed(seed)
- out.fill(numpy.random.random_sample(self.shape))
- elif value == VectorGeometry.RANDOM_INT:
- seed = kwargs.get('seed', None)
- if seed is not None:
- numpy.random.seed(seed)
- max_value = kwargs.get('max_value', 100)
- out.fill(numpy.random.randint(max_value,size=self.shape))
- else:
- raise ValueError('Value {} unknown'.format(value))
- return out
diff --git a/Wrappers/Python/ccpi/framework/__init__.py b/Wrappers/Python/ccpi/framework/__init__.py
index cae8988..94788a5 100755
--- a/Wrappers/Python/ccpi/framework/__init__.py
+++ b/Wrappers/Python/ccpi/framework/__init__.py
@@ -30,10 +30,10 @@ from functools import reduce
from .framework import DataContainer
from .framework import ImageData, AcquisitionData
from .framework import ImageGeometry, AcquisitionGeometry
+from .framework import VectorData, VectorGeometry
from .framework import find_key, message
from .framework import DataProcessor
from .framework import AX, PixelByPixelDataProcessor, CastDataContainer
from .BlockDataContainer import BlockDataContainer
from .BlockGeometry import BlockGeometry
from .TestData import TestData
-from .Vector import VectorGeometry, VectorData
diff --git a/Wrappers/Python/ccpi/framework/framework.py b/Wrappers/Python/ccpi/framework/framework.py
index 5768e7d..c27ad1e 100755
--- a/Wrappers/Python/ccpi/framework/framework.py
+++ b/Wrappers/Python/ccpi/framework/framework.py
@@ -506,8 +506,10 @@ class DataContainer(object):
#print ("axes {0}".format(axes))
cleaned = numpy.transpose(cleaned, axes).copy()
-
- return type(self)(cleaned , True, dimensions)
+ if cleaned.ndim > 1:
+ return type(self)(cleaned , True, dimensions)
+ else:
+ return VectorData(cleaned)
def fill(self, array, **dimension):
'''fills the internal numpy array with the one provided'''
@@ -1325,165 +1327,71 @@ class PixelByPixelDataProcessor(DataProcessor):
return y
+class VectorData(DataContainer):
+ '''DataContainer to contain 1D array'''
+ def __init__(self, array=None, **kwargs):
+ self.geometry = kwargs.get('geometry', None)
+ self.dtype = kwargs.get('dtype', numpy.float32)
+ if self.geometry is None:
+ if array is None:
+ raise ValueError('Please specify either a geometry or an array')
+ else:
+ if len(array.shape) > 1:
+ raise ValueError('Incompatible size: expected 1D got {}'.format(array.shape))
+ out = array
+ self.geometry = VectorGeometry(array.shape[0])
+ self.length = self.geometry.length
+ else:
+ self.length = self.geometry.length
+
+ if array is None:
+ out = numpy.zeros((self.length,), dtype=self.dtype)
+ else:
+ if self.length == array.shape[0]:
+ out = array
+ else:
+ raise ValueError('Incompatible size: expecting {} got {}'.format((self.length,), array.shape))
+ deep_copy = True
+ super(VectorData, self).__init__(out, deep_copy, None)
+
+class VectorGeometry(object):
+ '''Geometry describing VectorData to contain 1D array'''
+ RANDOM = 'random'
+ RANDOM_INT = 'random_int'
-if __name__ == '__main__':
- shape = (2,3,4,5)
- size = shape[0]
- for i in range(1, len(shape)):
- size = size * shape[i]
- #print("a refcount " , sys.getrefcount(a))
- a = numpy.asarray([i for i in range( size )])
- print("a refcount " , sys.getrefcount(a))
- a = numpy.reshape(a, shape)
- print("a refcount " , sys.getrefcount(a))
- ds = DataContainer(a, False, ['X', 'Y','Z' ,'W'])
- print("a refcount " , sys.getrefcount(a))
- print ("ds label {0}".format(ds.dimension_labels))
- subset = ['W' ,'X']
- b = ds.subset( subset )
- print("a refcount " , sys.getrefcount(a))
- print ("b label {0} shape {1}".format(b.dimension_labels,
- numpy.shape(b.as_array())))
- c = ds.subset(['Z','W','X'])
- print("a refcount " , sys.getrefcount(a))
-
- # Create a ImageData sharing the array with c
- volume0 = ImageData(c.as_array(), False, dimensions = c.dimension_labels)
- volume1 = ImageData(c, False)
-
- print ("volume0 {0} volume1 {1}".format(id(volume0.array),
- id(volume1.array)))
-
- # Create a ImageData copying the array from c
- volume2 = ImageData(c.as_array(), dimensions = c.dimension_labels)
- volume3 = ImageData(c)
-
- print ("volume2 {0} volume3 {1}".format(id(volume2.array),
- id(volume3.array)))
+ def __init__(self,
+ length):
- # single number DataSet
- sn = DataContainer(numpy.asarray([1]))
-
- ax = AX()
- ax.scalar = 2
- ax.set_input(c)
- #ax.apply()
- print ("ax in {0} out {1}".format(c.as_array().flatten(),
- ax.get_output().as_array().flatten()))
-
- cast = CastDataContainer(dtype=numpy.float32)
- cast.set_input(c)
- out = cast.get_output()
- out *= 0
- axm = AX()
- axm.scalar = 0.5
- axm.set_input_processor(cast)
- axm.get_output(out)
- #axm.apply()
- print ("axm in {0} out {1}".format(c.as_array(), axm.get_output().as_array()))
-
- # check out in DataSetProcessor
- #a = numpy.asarray([i for i in range( size )])
-
+ self.length = length
+ self.shape = (length, )
- # create a PixelByPixelDataProcessor
-
- #define a python function which will take only one input (the pixel value)
- pyfunc = lambda x: -x if x > 20 else x
- clip = PixelByPixelDataProcessor()
- clip.pyfunc = pyfunc
- clip.set_input(c)
- #clip.apply()
-
- print ("clip in {0} out {1}".format(c.as_array(), clip.get_output().as_array()))
-
- #dsp = DataProcessor()
- #dsp.set_input(ds)
- #dsp.input = a
- # pipeline
+
+ def clone(self):
+ '''returns a copy of VectorGeometry'''
+ return VectorGeometry(self.length)
- chain = AX()
- chain.scalar = 0.5
- chain.set_input_processor(ax)
- print ("chain in {0} out {1}".format(ax.get_output().as_array(), chain.get_output().as_array()))
-
- # testing arithmetic operations
-
- print (b)
- print ((b+1))
- print ((1+b))
-
- print (b)
- print ((b*2))
-
- print (b)
- print ((2*b))
-
- print (b)
- print ((b/2))
-
- print (b)
- print ((2/b))
-
- print (b)
- print ((b**2))
-
- print (b)
- print ((2**b))
-
- print (type(volume3 + 2))
-
- s = [i for i in range(3 * 4 * 4)]
- s = numpy.reshape(numpy.asarray(s), (3,4,4))
- sino = AcquisitionData( s )
-
- shape = (4,3,2)
- a = [i for i in range(2*3*4)]
- a = numpy.asarray(a)
- a = numpy.reshape(a, shape)
- print (numpy.shape(a))
- ds = DataContainer(a, True, ['X', 'Y','Z'])
- # this means that I expect the X to be of length 2 ,
- # y of length 3 and z of length 4
- subset = ['Y' ,'Z']
- b0 = ds.subset( subset )
- print ("shape b 3,2? {0}".format(numpy.shape(b0.as_array())))
- # expectation on b is that it is
- # 3x2 cut at z = 0
-
- subset = ['X' ,'Y']
- b1 = ds.subset( subset , Z=1)
- print ("shape b 2,3? {0}".format(numpy.shape(b1.as_array())))
-
-
+ def allocate(self, value=0, **kwargs):
+ '''allocates an VectorData according to the size expressed in the instance'''
+ self.dtype = kwargs.get('dtype', numpy.float32)
+ out = VectorData(geometry=self, dtype=self.dtype)
+ if isinstance(value, Number):
+ if value != 0:
+ out += value
+ else:
+ if value == VectorGeometry.RANDOM:
+ seed = kwargs.get('seed', None)
+ if seed is not None:
+ numpy.random.seed(seed)
+ out.fill(numpy.random.random_sample(self.shape))
+ elif value == VectorGeometry.RANDOM_INT:
+ seed = kwargs.get('seed', None)
+ if seed is not None:
+ numpy.random.seed(seed)
+ max_value = kwargs.get('max_value', 100)
+ out.fill(numpy.random.randint(max_value,size=self.shape))
+ else:
+ raise ValueError('Value {} unknown'.format(value))
+ return out
- # create VolumeData from geometry
- vgeometry = ImageGeometry(voxel_num_x=2, voxel_num_y=3, channels=2)
- vol = ImageData(geometry=vgeometry)
-
- sgeometry = AcquisitionGeometry(dimension=2, angles=numpy.linspace(0, 180, num=20),
- geom_type='parallel', pixel_num_v=3,
- pixel_num_h=5 , channels=2)
- sino = AcquisitionData(geometry=sgeometry)
- sino2 = sino.clone()
-
- a0 = numpy.asarray([i for i in range(2*3*4)])
- a1 = numpy.asarray([2*i for i in range(2*3*4)])
-
-
- ds0 = DataContainer(numpy.reshape(a0,(2,3,4)))
- ds1 = DataContainer(numpy.reshape(a1,(2,3,4)))
-
- numpy.testing.assert_equal(ds0.dot(ds1), a0.dot(a1))
-
- a2 = numpy.asarray([2*i for i in range(2*3*5)])
- ds2 = DataContainer(numpy.reshape(a2,(2,3,5)))
-
-# # it should fail if the shape is wrong
-# try:
-# ds2.dot(ds0)
-# self.assertTrue(False)
-# except ValueError as ve:
-# self.assertTrue(True)
diff --git a/Wrappers/Python/test/test_Operator.py b/Wrappers/Python/test/test_Operator.py
index 1ec7761..775b446 100644
--- a/Wrappers/Python/test/test_Operator.py
+++ b/Wrappers/Python/test/test_Operator.py
@@ -405,7 +405,7 @@ class TestBlockOperator(unittest.TestCase):
u = ig.allocate('random_int')
steps = [timer()]
i = 0
- n = 2.
+ n = 10.
t1 = t2 = 0
res = B.range_geometry().allocate()
@@ -456,7 +456,7 @@ class TestBlockOperator(unittest.TestCase):
i += 1
print ("Time difference ", t1,t2)
- self.assertGreater(t1,t2)
+ # self.assertGreater(t1,t2)
def test_BlockOperatorLinearValidity(self):
print ("test_BlockOperatorLinearValidity")
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-05 16:33:20 +0000