savu.plugins.unregistered.i18_loaders.base_i18_multi_modal_loader.BaseI18MultiModalLoader.__init__() - Code Metrics - DiamondLightSource/Savu - Measure and Improve Code Quality continuously with Scrutinizer

BaseI18MultiModalLoader.init() A
last analyzed 2022-08-17 15:44 UTC

↳ Parent: savu.plugins.unregistered.i18_loaders.base_i18_multi_modal_loader

Complexity

Conditions

Size

Total Lines	2
Code Lines	2

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	1
eloc	2
nop	2
dl	0
loc	2
rs	10
c	0
b	0
f	0

# Copyright 2014 Diamond Light Source Ltd.
#
# 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.

"""
.. module:: base_i18_multi_modal_loader
   :platform: Unix
   :synopsis: Contains a base class from which all multi-modal loaders are \
   derived.

.. moduleauthor:: Nicola Wadeson <[email protected]>

"""

import h5py
import logging
from savu.data.data_structures.data_add_ons import DataMapping

from savu.plugins.loaders.mapping_loaders.base_multi_modal_loader \
    import BaseMultiModalLoader


class BaseI18MultiModalLoader(BaseMultiModalLoader):
    def __init__(self, name='BaseI18MultiModalLoader'):
        super(BaseI18MultiModalLoader, self).__init__(name)

    def multi_modal_setup(self, ltype, name):
        # set up the file handles
        exp = self.exp
        data_obj = exp.create_data_object("in_data", name)
        data_obj.backing_file = \
            h5py.File(exp.meta_data.get("data_file"), 'r')
        f = data_obj.backing_file
        logging.debug("Creating file '%s' '%s'_entry",
                      data_obj.backing_file.filename, ltype)

        data_obj.meta_data.set(
            "mono_energy", f[self.parameters['monochromator']][()]/1e3)
        x = f[self.parameters['x']][()]

        if self.parameters['x'] is not None:
            if x.ndim > 1:
                data_obj.meta_data.set("x", x[0, :])
            else:
                data_obj.meta_data.set("x", x)

        if self.parameters['y'] is not None:
            y = f[self.parameters['y']][()]
            data_obj.meta_data.set("y", y)
        if self.parameters['rotation'] is not None:
            rotation_angle = f[self.parameters['rotation']][()]
            if rotation_angle.ndim > 1:
                rotation_angle = rotation_angle[:, 0]

            data_obj.meta_data.set("rotation_angle", rotation_angle)
        return data_obj

    def set_motors(self, data_obj, ltype):
        # now lets extract the map, if there is one!
        # to begin with
        data_obj.data_mapping = DataMapping()
        logging.debug("========="+ltype+"=========")
        motors = self.parameters['scan_pattern']
        data_obj.data_mapping.set_axes(self.parameters['scan_pattern'])
        nAxes = len(data_obj.get_shape())
        #logging.debug nAxes
        cts = 0
        chk = 0
        chk1 = 0
        motor_type = []
        labels = []
        fast_axis = self.parameters["fast_axis"]
        logging.debug("axes input are:"+str(motors))
        unknown_count = 0
        for ii in range(nAxes):
            # find the rotation axis
            try:
                data_axis = self.parameters[motors[ii]]# get that out the file
                logging.debug("the data axis is %s" % str(data_axis))
                if motors[ii]=="rotation":
                    data_obj.data_mapping._is_tomo = True
                    motor_type.append('rotation')
                    label = 'rotation_angle'
                    units = 'degrees'
                    logging.debug(ltype + " reader: %s", "is a tomo scan")
                elif motors[ii] in ["x","y"]:
                    cts += 1  # increase the order of the map
                    motor_type.append('translation')
                    if (motors[ii]==fast_axis):
                        label='x'
                    else:
                        label='y'
                    units = 'mm'
            except KeyError as e:
                #print("exception was ",str(e))
                #print("found no motor")
                motor_type.append('None')
                #now the detector axes
                if ltype =='fluo':
                    label = 'energy'
                    units = 'counts'
                elif ltype =='xrd':
                    if chk==0:
                        label = 'detector_x'
                    elif chk==1:
                        label = 'detector_y'
                    units = 'index'
                    chk=chk+1

            except IndexError:
                '''
                some additional singleton dimensions have been added in the latest mapping project stuff on I18
                This fixes that.
                '''
                if ltype =='xrd':
                    if chk1 == 0:
                        label = 'detector_x'
                    elif chk1 == 1:
                        label = 'detector_y'
                    units = 'pixels'
                    chk1=chk1+1
                else:
                    label = 'unknown_%s' % unknown_count
                    units = 'unknown'
                    unknown_count += 1
            except:
                raise

            labels.append(label+'.'+units)

        if not motors:
            logging.debug("%s reader: No maps found!", ltype)
        #logging.debug labels
        data_obj.set_axis_labels(*tuple(labels))
        data_obj.data_mapping.set_motors(motors)
        data_obj.data_mapping.set_motor_type(motor_type)
        if (cts):
            data_obj.data_mapping._is_map = cts
        else:
            logging.debug("'%s' reader: No translations found!", ltype)
            pass
        logging.debug("axis labels:"+str(labels))
        logging.debug("motor_type:"+str(motor_type))

    def add_patterns_based_on_acquisition(self, data_obj, ltype):
        motor_type = data_obj.data_mapping.get_motor_type()
        projection = []
        for item, key in enumerate(motor_type):
            if key == 'translation':
                projection.append(item)
#                 logging.debug projection
            elif key == 'rotation':
                rotation = item
        dims = list(range(len(data_obj.get_shape())))
        if data_obj.data_mapping._is_map:
            proj_dir = tuple(projection)
            data_obj.add_pattern("PROJECTION", core_dims=proj_dir,
                                 slice_dims=tuple(set(dims) - set(proj_dir)))

        if data_obj.data_mapping._is_tomo:
            #rotation and fast axis
            sino_dir = (rotation, proj_dir[-1])

            slice_dims = tuple(set(dims) - set(sino_dir))
            if slice_dims:
                data_obj.add_pattern("SINOGRAM", core_dims=sino_dir,
                                     slice_dims=slice_dims)

        if ltype == 'fluo':
            spec_core = (-1,) # it will always be this
            spec_slice = tuple(dims[:-1])
            data_obj.add_pattern("SPECTRUM", core_dims=spec_core,
                                 slice_dims=spec_slice)


        if ltype == 'xrd':
            diff_core = (-2,-1) # it will always be this
            diff_slice = tuple(dims[:-2])
            data_obj.add_pattern("DIFFRACTION", core_dims=diff_core,
                                 slice_dims=diff_slice)

        if ltype == 'monitor':
            # this is needed for I0 corrections of single sinogram ND data
            channel_core = (dims[-1],)
            channel_slice = tuple(dims[:-1])
            data_obj.add_pattern("CHANNEL", core_dims=channel_core,
                        slice_dims=channel_slice)



1			# Copyright 2014 Diamond Light Source Ltd.
2			#
3			# Licensed under the Apache License, Version 2.0 (the "License");
4			# you may not use this file except in compliance with the License.
5			# You may obtain a copy of the License at
6			#
7			# http://www.apache.org/licenses/LICENSE-2.0
8			#
9			# Unless required by applicable law or agreed to in writing, software
10			# distributed under the License is distributed on an "AS IS" BASIS,
11			# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12			# See the License for the specific language governing permissions and
13			# limitations under the License.
14
15			"""
16			.. module:: base_i18_multi_modal_loader
17			:platform: Unix
18			:synopsis: Contains a base class from which all multi-modal loaders are \
19			derived.
20
21			.. moduleauthor:: Nicola Wadeson <[email protected]>
22
23			"""
24
25			import h5py
26			import logging
27			from savu.data.data_structures.data_add_ons import DataMapping
28
29			from savu.plugins.loaders.mapping_loaders.base_multi_modal_loader \
30			import BaseMultiModalLoader
31
32
33			class BaseI18MultiModalLoader(BaseMultiModalLoader):
34			def __init__(self, name='BaseI18MultiModalLoader'):
35			super(BaseI18MultiModalLoader, self).__init__(name)
36
37			def multi_modal_setup(self, ltype, name):
38			# set up the file handles
39			exp = self.exp
40			data_obj = exp.create_data_object("in_data", name)
41			data_obj.backing_file = \
42			h5py.File(exp.meta_data.get("data_file"), 'r')
43			f = data_obj.backing_file
44			logging.debug("Creating file '%s' '%s'_entry",
45			data_obj.backing_file.filename, ltype)
46
47			data_obj.meta_data.set(
48			"mono_energy", f[self.parameters['monochromator']][()]/1e3)
49			x = f[self.parameters['x']][()]
50
51			if self.parameters['x'] is not None:
52			if x.ndim > 1:
53			data_obj.meta_data.set("x", x[0, :])
54			else:
55			data_obj.meta_data.set("x", x)
56
57			if self.parameters['y'] is not None:
58			y = f[self.parameters['y']][()]
59			data_obj.meta_data.set("y", y)
60			if self.parameters['rotation'] is not None:
61			rotation_angle = f[self.parameters['rotation']][()]
62			if rotation_angle.ndim > 1:
63			rotation_angle = rotation_angle[:, 0]
64
65			data_obj.meta_data.set("rotation_angle", rotation_angle)
66			return data_obj
67
68			def set_motors(self, data_obj, ltype):
69			# now lets extract the map, if there is one!
70			# to begin with
71			data_obj.data_mapping = DataMapping()
72			logging.debug("========="+ltype+"=========")
73			motors = self.parameters['scan_pattern']
74			data_obj.data_mapping.set_axes(self.parameters['scan_pattern'])
75			nAxes = len(data_obj.get_shape())
76			#logging.debug nAxes
77			cts = 0
78			chk = 0
79			chk1 = 0
80			motor_type = []
81			labels = []
82			fast_axis = self.parameters["fast_axis"]
83			logging.debug("axes input are:"+str(motors))
84			unknown_count = 0
85			for ii in range(nAxes):
86			# find the rotation axis
87			try:
88			data_axis = self.parameters[motors[ii]]# get that out the file
89			logging.debug("the data axis is %s" % str(data_axis))
90			if motors[ii]=="rotation":
91			data_obj.data_mapping._is_tomo = True
92			motor_type.append('rotation')
93			label = 'rotation_angle'
94			units = 'degrees'
95			logging.debug(ltype + " reader: %s", "is a tomo scan")
96			elif motors[ii] in ["x","y"]:
97			cts += 1 # increase the order of the map
98			motor_type.append('translation')
99			if (motors[ii]==fast_axis):
100			label='x'
101			else:
102			label='y'
103			units = 'mm'
104			except KeyError as e:
105			#print("exception was ",str(e))
106			#print("found no motor")
107			motor_type.append('None')
108			#now the detector axes
109			if ltype =='fluo':
110			label = 'energy'
111			units = 'counts'
112			elif ltype =='xrd':
113			if chk==0:
114			label = 'detector_x'
115			elif chk==1:
116			label = 'detector_y'
117			units = 'index'
118			chk=chk+1
119
120			except IndexError:
121			'''
122			some additional singleton dimensions have been added in the latest mapping project stuff on I18
123			This fixes that.
124			'''
125			if ltype =='xrd':
126			if chk1 == 0:
127			label = 'detector_x'
128			elif chk1 == 1:
129			label = 'detector_y'
130			units = 'pixels'
131			chk1=chk1+1
132			else:
133			label = 'unknown_%s' % unknown_count
134			units = 'unknown'
135			unknown_count += 1
136			except:
137			raise
138
139			labels.append(label+'.'+units)
			0 ignored issues – show introduced 2021-02-25 17:14 UTC by Report Bug Copy Issue Report The variable `units` does not seem to be defined for all execution paths. Loading history... introduced 2021-02-25 17:14 UTC by Report Bug Copy Issue Report The variable `label` does not seem to be defined for all execution paths. Loading history...
140			if not motors:
141			logging.debug("%s reader: No maps found!", ltype)
142			#logging.debug labels
143			data_obj.set_axis_labels(*tuple(labels))
144			data_obj.data_mapping.set_motors(motors)
145			data_obj.data_mapping.set_motor_type(motor_type)
146			if (cts):
147			data_obj.data_mapping._is_map = cts
148			else:
149			logging.debug("'%s' reader: No translations found!", ltype)
150			pass
151			logging.debug("axis labels:"+str(labels))
152			logging.debug("motor_type:"+str(motor_type))
153
154			def add_patterns_based_on_acquisition(self, data_obj, ltype):
155			motor_type = data_obj.data_mapping.get_motor_type()
156			projection = []
157			for item, key in enumerate(motor_type):
158			if key == 'translation':
159			projection.append(item)
160			# logging.debug projection
161			elif key == 'rotation':
162			rotation = item
163			dims = list(range(len(data_obj.get_shape())))
164			if data_obj.data_mapping._is_map:
165			proj_dir = tuple(projection)
166			data_obj.add_pattern("PROJECTION", core_dims=proj_dir,
167			slice_dims=tuple(set(dims) - set(proj_dir)))
168
169			if data_obj.data_mapping._is_tomo:
170			#rotation and fast axis
171			sino_dir = (rotation, proj_dir[-1])
			0 ignored issues – show introduced 2021-02-25 17:14 UTC by Report Bug Copy Issue Report The variable `proj_dir` does not seem to be defined in case `data_obj.data_mapping._is_map` on line `164` is `False`. Are you sure this can never be the case? Loading history... introduced 2021-02-25 17:14 UTC by Report Bug Copy Issue Report The variable `rotation` does not seem to be defined for all execution paths. Loading history...
172			slice_dims = tuple(set(dims) - set(sino_dir))
173			if slice_dims:
174			data_obj.add_pattern("SINOGRAM", core_dims=sino_dir,
175			slice_dims=slice_dims)
176
177			if ltype == 'fluo':
178			spec_core = (-1,) # it will always be this
179			spec_slice = tuple(dims[:-1])
180			data_obj.add_pattern("SPECTRUM", core_dims=spec_core,
181			slice_dims=spec_slice)
182
183
184			if ltype == 'xrd':
185			diff_core = (-2,-1) # it will always be this
186			diff_slice = tuple(dims[:-2])
187			data_obj.add_pattern("DIFFRACTION", core_dims=diff_core,
188			slice_dims=diff_slice)
189
190			if ltype == 'monitor':
191			# this is needed for I0 corrections of single sinogram ND data
192			channel_core = (dims[-1],)
193			channel_slice = tuple(dims[:-1])
194			data_obj.add_pattern("CHANNEL", core_dims=channel_core,
195			slice_dims=channel_slice)
196
197

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BaseI18MultiModalLoader.__init__() A last analyzed 2022-08-17 15:44 UTC

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BaseI18MultiModalLoader.init() A
last analyzed 2022-08-17 15:44 UTC