55import pathlib
66import time
77from src .wrappers .OsipiBase import OsipiBase
8- from conftest import eng
98#run using python -m pytest from the root folder
109
1110
@@ -31,50 +30,24 @@ def tolerances_helper(tolerances, data):
3130 tolerances ["atol" ] = tolerances .get ("atol" , {"f" : 2e-1 , "D" : 5e-4 , "Dp" : 4e-2 })
3231 return tolerances
3332
34- def data_ivim_fit_saved ():
35- # Find the algorithms from algorithms.json
36- file = pathlib .Path (__file__ )
37- algorithm_path = file .with_name ('algorithms.json' )
38- with algorithm_path .open () as f :
39- algorithm_information = json .load (f )
40-
41- # Load generic test data generated from the included phantom: phantoms/MR_XCAT_qMRI
42- generic = file .with_name ('generic.json' )
43- with generic .open () as f :
44- all_data = json .load (f )
45-
46- algorithms = algorithm_information ["algorithms" ]
47- bvals = all_data .pop ('config' )
48- bvals = bvals ['bvalues' ]
49- for algorithm in algorithms :
50- first = True
51- for name , data in all_data .items ():
52- algorithm_dict = algorithm_information .get (algorithm , {})
53- xfail = {"xfail" : name in algorithm_dict .get ("xfail_names" , {}),
54- "strict" : algorithm_dict .get ("xfail_names" , {}).get (name , True )}
55- kwargs = algorithm_dict .get ("options" , {})
56- tolerances = algorithm_dict .get ("tolerances" , {})
57- skiptime = False
58- if first == True :
59- if algorithm_dict .get ("fail_first_time" , {}) == True :
60- skiptime = True
61- first = False
62- if algorithm_dict .get ("requieres_matlab" , {}) == True :
63- if eng is None :
64- continue
65- else :
66- kwargs = {** kwargs ,'eng' : eng }
67- yield name , bvals , data , algorithm , xfail , kwargs , tolerances , skiptime
68-
69- @pytest .mark .parametrize ("name, bvals, data, algorithm, xfail, kwargs, tolerances, skiptime" , data_ivim_fit_saved ())
70- def test_ivim_fit_saved (name , bvals , data , algorithm , xfail , kwargs , tolerances ,skiptime , request , record_property ):
33+ def test_ivim_fit_saved (data_ivim_fit_saved , eng , request , record_property ):
34+ name , bvals , data , algorithm , xfail , kwargs , tolerances , skiptime , requires_matlab = data_ivim_fit_saved
35+ max_time = 0.5
36+ if requires_matlab :
37+ max_time = 2
38+ if eng is None :
39+ print ('test is here' )
40+ pytest .skip (reason = "Running without matlab; if Matlab is available please run pytest --withmatlab" )
41+ else :
42+ print ('test is not here' )
43+ kwargs = {** kwargs , 'eng' : eng }
7144 if xfail ["xfail" ]:
7245 mark = pytest .mark .xfail (reason = "xfail" , strict = xfail ["strict" ])
7346 request .node .add_marker (mark )
7447 signal = signal_helper (data ["data" ])
7548 tolerances = tolerances_helper (tolerances , data )
76- start_time = time .time () # Record the start time
7749 fit = OsipiBase (algorithm = algorithm , ** kwargs )
50+ start_time = time .time () # Record the start time
7851 fit_result = fit .osipi_fit (signal , bvals )
7952 elapsed_time = time .time () - start_time # Calculate elapsed time
8053 def to_list_if_needed (value ):
@@ -99,29 +72,18 @@ def to_list_if_needed(value):
9972 npt .assert_allclose (fit_result ['Dp' ],data ['Dp' ], rtol = tolerances ["rtol" ]["Dp" ], atol = tolerances ["atol" ]["Dp" ])
10073 #assert fit_result['D'] < fit_result['Dp'], f"D {fit_result['D']} is larger than D* {fit_result['Dp']} for {name}"
10174 if not skiptime :
102- assert elapsed_time < 0.5 , f"Algorithm { name } { elapsed_time } #less than 0.5 seconds per voxel
103-
104-
105- def algorithmlist ():
106- # Find the algorithms from algorithms.json
107- file = pathlib .Path (__file__ )
108- algorithm_path = file .with_name ('algorithms.json' )
109- with algorithm_path .open () as f :
110- algorithm_information = json .load (f )
111- algorithms = algorithm_information ["algorithms" ]
112- for algorithm in algorithms :
113- algorithm_dict = algorithm_information .get (algorithm , {})
114- args = {}
115- if algorithm_dict .get ("requieres_matlab" , {}) == True :
116- if eng is None :
117- continue
118- else :
119- args = {** args , 'eng' : eng }
120- yield algorithm , args
121-
122- @pytest .mark .parametrize ("algorithm, args" , algorithmlist ())
123- def test_default_bounds_and_initial_guesses (algorithm , args ):
124- fit = OsipiBase (algorithm = algorithm ,** args )
75+ assert elapsed_time < max_time , f"Algorithm { name } { elapsed_time } #less than 0.5 seconds per voxel
76+
77+ def test_default_bounds_and_initial_guesses (algorithmlist ,eng ):
78+ algorithm , requires_matlab = algorithmlist
79+ if requires_matlab :
80+ if eng is None :
81+ pytest .skip (reason = "Running without matlab; if Matlab is available please run pytest --withmatlab" )
82+ else :
83+ kwargs = {'eng' : eng }
84+ else :
85+ kwargs = {}
86+ fit = OsipiBase (algorithm = algorithm ,** kwargs )
12587 #assert fit.bounds is not None, f"For {algorithm}, there is no default fit boundary"
12688 #assert fit.initial_guess is not None, f"For {algorithm}, there is no default fit initial guess"
12789 if fit .use_bounds :
@@ -141,38 +103,13 @@ def test_default_bounds_and_initial_guesses(algorithm, args):
141103 assert 0.9 <= fit .initial_guess [3 ] <= 1.1 , f"For { algorithm } { fit .initial_guess [3 ]}
142104
143105
144- def bound_input ():
145- # Find the algorithms from algorithms.json
146- file = pathlib .Path (__file__ )
147- algorithm_path = file .with_name ('algorithms.json' )
148- with algorithm_path .open () as f :
149- algorithm_information = json .load (f )
150-
151- # Load generic test data generated from the included phantom: phantoms/MR_XCAT_qMRI
152- generic = file .with_name ('generic.json' )
153- with generic .open () as f :
154- all_data = json .load (f )
155-
156- algorithms = algorithm_information ["algorithms" ]
157- bvals = all_data .pop ('config' )
158- bvals = bvals ['bvalues' ]
159- for name , data in all_data .items ():
160- for algorithm in algorithms :
161- algorithm_dict = algorithm_information .get (algorithm , {})
162- xfail = {"xfail" : name in algorithm_dict .get ("xfail_names" , {}),
163- "strict" : algorithm_dict .get ("xfail_names" , {}).get (name , True )}
164- kwargs = algorithm_dict .get ("options" , {})
165- tolerances = algorithm_dict .get ("tolerances" , {})
166- if algorithm_dict .get ("requieres_matlab" , {}) == True :
167- if eng is None :
168- continue
169- else :
170- kwargs = {** kwargs , 'eng' : eng }
171- yield name , bvals , data , algorithm , xfail , kwargs , tolerances
172-
173-
174- @pytest .mark .parametrize ("name, bvals, data, algorithm, xfail, kwargs, tolerances" , bound_input ())
175- def test_bounds (name , bvals , data , algorithm , xfail , kwargs , tolerances , request ):
106+ def test_bounds (bound_input , eng ):
107+ name , bvals , data , algorithm , xfail , kwargs , tolerances , requires_matlab = bound_input
108+ if requires_matlab :
109+ if eng is None :
110+ pytest .skip (reason = "Running without matlab; if Matlab is available please run pytest --withmatlab" )
111+ else :
112+ kwargs = {** kwargs , 'eng' : eng }
176113 bounds = ([0.0008 , 0.2 , 0.01 , 1.1 ], [0.0012 , 0.3 , 0.02 , 1.3 ])
177114 # deliberately have silly bounds to see whether they are used
178115 fit = OsipiBase (algorithm = algorithm , bounds = bounds , initial_guess = [0.001 , 0.25 , 0.015 , 1.2 ], ** kwargs )
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