polarpy.polar2hdf5.polar_spectra_to_hdf5() - Code Metrics - Inspection of "Merge pull request #1 from grburgess/new_response" - grburgess/polarpy - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Push — master ( fd2cae...1dc21f )

by J. Michael

created 2018-08-08 14:16 UTC

polarpy.polar2hdf5.polar_spectra_to_hdf5() B

↳ Parent: polarpy.polar2hdf5

Complexity

Conditions

Size

Total Lines	81
Code Lines	32

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	7
eloc	32
nop	3
dl	0
loc	81
rs	7.712
c	0
b	0
f	0

How to fix Long Method

import h5py
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
import numpy as np



try:
    import ROOT
    from threeML.io.cern_root_utils.io_utils import open_ROOT_file
    from threeML.io.cern_root_utils.tobject_to_numpy import tree_to_ndarray, th2_to_arrays

    has_root = True


except(ImportError):


    has_root = False


    


if has_root:

    def polar_polarization_to_hdf5(polarization_root_file, hdf5_out_file):

        """

        :param polarization_root_file: The ROOT file from which to build the response
        :param hdf5_out_file: The output HDF5 file name
        """
        energy = []
        degree = []
        angle = []

        energy_str = []
        degree_str = []
        angle_str = []

        

        with open_ROOT_file(polarization_root_file) as f:


            tmp = [key.GetName() for key in f.GetListOfKeys()]
            tmp = filter(lambda x: 'sim' in x, tmp)
            for tmp2 in tmp:
                _, x, y, z = tmp2.split('_')


                energy.append(float(x))
                degree.append(float(y))
                angle.append(float(z))

                energy_str.append(x)
                degree_str.append(y)
                angle_str.append(z)


                


            energy = np.array(np.unique(energy))
            degree = np.array(np.unique(degree))
            angle  = np.array(np.unique(angle))


            energy_str = np.array(np.unique(energy_str))
            degree_str = np.array(np.unique(degree_str))
            angle_str  = np.array(np.unique(angle_str))


            # just to get the bins
            # must change this from ints later

            file_string = 'sim_%s_%s_%s' % (energy_str[1], degree_str[1], angle_str[1])

            bins, _, hist = th2_to_arrays(f.Get(file_string))

            out_matrix = np.zeros((len(energy), len(angle), len(degree), len(hist)))

            with h5py.File(hdf5_out_file, 'w', libver='latest') as database:

                for i,x in enumerate(energy_str):




                    for j, y in enumerate(angle_str):




                        for k, z in enumerate(degree_str):


                            file_string = 'sim_%s_%s_%s' % (x, z, y)

                            _ , _, hist = th2_to_arrays(f.Get(file_string))


                            out_matrix[i,j,k,:] = hist




                database.create_dataset('matrix',data=out_matrix,compression='lzf')



                if np.min(bins) < 0:
                    # we will try to automatically correct for the badly specified bins
                    bins = np.array(bins)

                    bins += -np.min(bins)

                    assert np.min(bins) >=0, 'The scattering bins have egdes less than zero'

                    assert np.max(bins) <=360, 'The scattering bins have egdes greater than 360'


                    

                

                database.create_dataset('bins', data=bins, compression='lzf')
                database.create_dataset('pol_ang', data=angle, compression='lzf')
                database.create_dataset('pol_deg', data=degree, compression='lzf')
                database.create_dataset('energy',data=energy,compression='lzf')


    def polar_spectra_to_hdf5(polar_root_file, polar_rsp_root_file, hdf5_out_file):

        """

        :param polar_root_file: The spectral ROOT file
        :param polar_rsp_root_file: The response ROOT file
        :param hdf5_out_file: the name of the output HDF5 file
        """

        # extract the info from the crappy root file

        with h5py.File(hdf5_out_file, 'w') as outfile:

            # first we do the RSP

            rsp_grp = outfile.create_group('rsp')

            with open_ROOT_file(polar_rsp_root_file) as f:


                matrix = th2_to_arrays(f.Get('rsp'))[-1]

                rsp_grp.create_dataset('matrix', data=matrix, compression='lzf')

                ebounds = th2_to_arrays(f.Get('EM_bounds'))[-1]

                rsp_grp.create_dataset('ebounds', data=ebounds, compression='lzf')

                mc_low = th2_to_arrays(f.Get('ER_low'))[-1]

                rsp_grp.create_dataset('mc_low', data=mc_low, compression='lzf')

                mc_high = th2_to_arrays(f.Get('ER_high'))[-1]

                rsp_grp.create_dataset('mc_high', data=mc_high, compression='lzf')

            # now we get the spectral informations
            keys_to_use = ['polar_out']

            f = ROOT.TFile(polar_root_file)


            extra_grp = outfile.create_group('extras')

            for key in f.GetListOfKeys():

                name = key.GetName()

                if name not in keys_to_use:
                    try:

                        # first we see if it is a TTree and then
                        # add a new group and attach its data

                        tree = tree_to_ndarray(f.Get(name))

                        new_grp = extra_grp.create_group(name)

                        for new_name in tree.dtype.names:
                            new_grp.create_dataset(new_name, data=tree[new_name], compression='lzf')

                    except:


                        # in this case we just want the actual data

                        data = th2_to_arrays(f.Get(name))[-1]

                        extra_grp.create_dataset(name, data=data, compression='lzf')

            # now we will deal with the data that is important

            tmp = tree_to_ndarray(f.Get('polar_out'))

            outfile.create_dataset('energy', data=tmp['Energy'], compression='lzf')

            outfile.create_dataset('scatter_angle', data=tmp['scatter_angle'], compression='lzf')
            

            outfile.create_dataset('dead_ratio', data=tmp['dead_ratio'], compression='lzf')

            outfile.create_dataset('time', data=tmp['tunix'], compression='lzf')

            

            

            f.Close()


1			import h5py
			0 ignored issues – show Coding Style introduced 2018-08-08 07:31 UTC by Report Bug Copy Issue Report This module should have a docstring. The coding style of this project requires that you add a docstring to this code element. Below, you find an example for methods: class SomeClass: def some_method(self): """Do x and return foo.""" If you would like to know more about docstrings, we recommend to read PEP-257: Docstring Conventions. Loading history... introduced 2018-08-08 07:31 UTC by Report Bug Copy Issue Report Unable to import 'h5py' Loading history...
2			import numpy as np
			0 ignored issues – show introduced 2018-08-08 07:31 UTC by Report Bug Copy Issue Report Unable to import 'numpy' Loading history...
3
4
5			try:
6			import ROOT
7			from threeML.io.cern_root_utils.io_utils import open_ROOT_file
8			from threeML.io.cern_root_utils.tobject_to_numpy import tree_to_ndarray, th2_to_arrays
9
10			has_root = True
			0 ignored issues – show Coding Style Naming introduced 2018-08-08 07:31 UTC by Report Bug Copy Issue Report The name `has_root` does not conform to the constant naming conventions (`(([A-Z_][A-Z0-9_])\|(__.__))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
11
12			except(ImportError):
			0 ignored issues – show Unused Code Coding Style introduced 2018-08-08 07:31 UTC by Report Bug Copy Issue Report There is an unnecessary parenthesis after `except`. Loading history...
13
14			has_root = False
			0 ignored issues – show Coding Style Naming introduced 2018-08-08 07:31 UTC by Report Bug Copy Issue Report The name `has_root` does not conform to the constant naming conventions (`(([A-Z_][A-Z0-9_])\|(__.__))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
15
16
			0 ignored issues – show Coding Style introduced 2018-08-08 07:31 UTC by Report Bug Copy Issue Report Trailing whitespace Loading history...
17
18			if has_root:
19
20			def polar_polarization_to_hdf5(polarization_root_file, hdf5_out_file):
			0 ignored issues – show Comprehensibility introduced 2018-08-08 07:31 UTC by Report Bug Copy Issue Report This function exceeds the maximum number of variables (23/15). Loading history...
21			"""
22
23			:param polarization_root_file: The ROOT file from which to build the response
24			:param hdf5_out_file: The output HDF5 file name
25			"""
26			energy = []
27			degree = []
28			angle = []
29
30			energy_str = []
31			degree_str = []
32			angle_str = []
33
34
			0 ignored issues – show Coding Style introduced 2018-08-08 14:25 UTC by Report Bug Copy Issue Report Trailing whitespace Loading history...
35			with open_ROOT_file(polarization_root_file) as f:
			0 ignored issues – show Coding Style Naming introduced 2018-08-08 07:31 UTC by Report Bug Copy Issue Report The name `f` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
36
37			tmp = [key.GetName() for key in f.GetListOfKeys()]
38			tmp = filter(lambda x: 'sim' in x, tmp)
39			for tmp2 in tmp:
40			_, x, y, z = tmp2.split('_')
			0 ignored issues – show Coding Style Naming introduced 2018-08-08 07:31 UTC by Report Bug Copy Issue Report The name `x` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history... Coding Style Naming introduced 2018-08-08 07:31 UTC by Report Bug Copy Issue Report The name `y` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history... Coding Style Naming introduced 2018-08-08 07:31 UTC by Report Bug Copy Issue Report The name `z` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
41
42			energy.append(float(x))
43			degree.append(float(y))
44			angle.append(float(z))
45
46			energy_str.append(x)
47			degree_str.append(y)
48			angle_str.append(z)
49
50
51
			0 ignored issues – show Coding Style introduced 2018-08-08 14:25 UTC by Report Bug Copy Issue Report Trailing whitespace Loading history...
52
53			energy = np.array(np.unique(energy))
54			degree = np.array(np.unique(degree))
55			angle = np.array(np.unique(angle))
			0 ignored issues – show Coding Style introduced 2018-08-08 14:25 UTC by Report Bug Copy Issue Report Exactly one space required before assignment Loading history...
56
57			energy_str = np.array(np.unique(energy_str))
58			degree_str = np.array(np.unique(degree_str))
59			angle_str = np.array(np.unique(angle_str))
			0 ignored issues – show Coding Style introduced 2018-08-08 14:25 UTC by Report Bug Copy Issue Report Exactly one space required before assignment Loading history...
60
61			# just to get the bins
62			# must change this from ints later
63
64			file_string = 'sim_%s_%s_%s' % (energy_str[1], degree_str[1], angle_str[1])
65
66			bins, _, hist = th2_to_arrays(f.Get(file_string))
67
68			out_matrix = np.zeros((len(energy), len(angle), len(degree), len(hist)))
69
70			with h5py.File(hdf5_out_file, 'w', libver='latest') as database:
71
72			for i,x in enumerate(energy_str):
			0 ignored issues – show Coding Style introduced 2018-08-08 14:25 UTC by Report Bug Copy Issue Report Exactly one space required after comma Loading history... Coding Style Naming introduced 2018-08-08 14:25 UTC by Report Bug Copy Issue Report The name `x` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
73
74
75
76			for j, y in enumerate(angle_str):
			0 ignored issues – show Coding Style Naming introduced 2018-08-08 14:25 UTC by Report Bug Copy Issue Report The name `y` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
77
78
79
80			for k, z in enumerate(degree_str):
			0 ignored issues – show Coding Style Naming introduced 2018-08-08 14:25 UTC by Report Bug Copy Issue Report The name `z` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
81
82			file_string = 'sim_%s_%s_%s' % (x, z, y)
83
84			_ , _, hist = th2_to_arrays(f.Get(file_string))
			0 ignored issues – show Coding Style introduced 2018-08-08 14:25 UTC by Report Bug Copy Issue Report No space allowed before comma Loading history...
85
86			out_matrix[i,j,k,:] = hist
			0 ignored issues – show Coding Style introduced 2018-08-08 14:25 UTC by Report Bug Copy Issue Report Exactly one space required after comma Loading history...
87
88
89
90			database.create_dataset('matrix',data=out_matrix,compression='lzf')
			0 ignored issues – show Coding Style introduced 2018-08-08 14:25 UTC by Report Bug Copy Issue Report Exactly one space required after comma Loading history...
91
92
93			if np.min(bins) < 0:
94			# we will try to automatically correct for the badly specified bins
95			bins = np.array(bins)
96
97			bins += -np.min(bins)
98
99			assert np.min(bins) >=0, 'The scattering bins have egdes less than zero'
			0 ignored issues – show Coding Style introduced 2018-08-08 07:31 UTC by Report Bug Copy Issue Report Exactly one space required after comparison Loading history...
100			assert np.max(bins) <=360, 'The scattering bins have egdes greater than 360'
			0 ignored issues – show Coding Style introduced 2018-08-08 07:31 UTC by Report Bug Copy Issue Report Exactly one space required after comparison Loading history...
101
102
			0 ignored issues – show Coding Style introduced 2018-08-08 07:31 UTC by Report Bug Copy Issue Report Trailing whitespace Loading history...
103
			0 ignored issues – show Coding Style introduced 2018-08-08 07:31 UTC by Report Bug Copy Issue Report Trailing whitespace Loading history...
104			database.create_dataset('bins', data=bins, compression='lzf')
105			database.create_dataset('pol_ang', data=angle, compression='lzf')
106			database.create_dataset('pol_deg', data=degree, compression='lzf')
107			database.create_dataset('energy',data=energy,compression='lzf')
			0 ignored issues – show Coding Style introduced 2018-08-08 14:25 UTC by Report Bug Copy Issue Report Exactly one space required after comma Loading history...
108
109			def polar_spectra_to_hdf5(polar_root_file, polar_rsp_root_file, hdf5_out_file):
			0 ignored issues – show Comprehensibility introduced 2018-08-08 07:31 UTC by Report Bug Copy Issue Report This function exceeds the maximum number of variables (19/15). Loading history...
110			"""
111
112			:param polar_root_file: The spectral ROOT file
113			:param polar_rsp_root_file: The response ROOT file
114			:param hdf5_out_file: the name of the output HDF5 file
115			"""
116
117			# extract the info from the crappy root file
118
119			with h5py.File(hdf5_out_file, 'w') as outfile:
120
121			# first we do the RSP
122
123			rsp_grp = outfile.create_group('rsp')
124
125			with open_ROOT_file(polar_rsp_root_file) as f:
			0 ignored issues – show Coding Style Naming introduced 2018-08-08 07:31 UTC by Report Bug Copy Issue Report The name `f` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
126
127			matrix = th2_to_arrays(f.Get('rsp'))[-1]
128
129			rsp_grp.create_dataset('matrix', data=matrix, compression='lzf')
130
131			ebounds = th2_to_arrays(f.Get('EM_bounds'))[-1]
132
133			rsp_grp.create_dataset('ebounds', data=ebounds, compression='lzf')
134
135			mc_low = th2_to_arrays(f.Get('ER_low'))[-1]
136
137			rsp_grp.create_dataset('mc_low', data=mc_low, compression='lzf')
138
139			mc_high = th2_to_arrays(f.Get('ER_high'))[-1]
140
141			rsp_grp.create_dataset('mc_high', data=mc_high, compression='lzf')
142
143			# now we get the spectral informations
144			keys_to_use = ['polar_out']
145
146			f = ROOT.TFile(polar_root_file)
			0 ignored issues – show Coding Style Naming introduced 2018-08-08 07:31 UTC by Report Bug Copy Issue Report The name `f` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
147
148			extra_grp = outfile.create_group('extras')
149
150			for key in f.GetListOfKeys():
151
152			name = key.GetName()
153
154			if name not in keys_to_use:
155			try:
156
157			# first we see if it is a TTree and then
158			# add a new group and attach its data
159
160			tree = tree_to_ndarray(f.Get(name))
161
162			new_grp = extra_grp.create_group(name)
163
164			for new_name in tree.dtype.names:
165			new_grp.create_dataset(new_name, data=tree[new_name], compression='lzf')
166
167			except:
			0 ignored issues – show Coding Style Best Practice introduced 2018-08-08 07:31 UTC by Report Bug Copy Issue Report General except handlers without types should be used sparingly. Typically, you would use general except handlers when you intend to specifically handle all types of errors, f.e. when logging. Otherwise, such general error handlers can mask errors in your application that you want to know of. Loading history...
168
169			# in this case we just want the actual data
170
171			data = th2_to_arrays(f.Get(name))[-1]
172
173			extra_grp.create_dataset(name, data=data, compression='lzf')
174
175			# now we will deal with the data that is important
176
177			tmp = tree_to_ndarray(f.Get('polar_out'))
178
179			outfile.create_dataset('energy', data=tmp['Energy'], compression='lzf')
180
181			outfile.create_dataset('scatter_angle', data=tmp['scatter_angle'], compression='lzf')
182
			0 ignored issues – show Coding Style introduced 2018-08-08 07:31 UTC by Report Bug Copy Issue Report Trailing whitespace Loading history...
183			outfile.create_dataset('dead_ratio', data=tmp['dead_ratio'], compression='lzf')
184
185			outfile.create_dataset('time', data=tmp['tunix'], compression='lzf')
186
187
			0 ignored issues – show Coding Style introduced 2018-08-08 07:31 UTC by Report Bug Copy Issue Report Trailing whitespace Loading history...
188
			0 ignored issues – show Coding Style introduced 2018-08-08 07:31 UTC by Report Bug Copy Issue Report Trailing whitespace Loading history...
189			f.Close()
190

grburgess / polarpy

Push — master ( fd2cae...1dc21f )

polarpy.polar2hdf5.polar_spectra_to_hdf5() B

Complexity

Size

Duplication

Importance

How to fix Long Method

Long Method

Duplication Side-by-Side

Filter issues like