Merge pull request #13 from canlab/unittests

Final project changes

Ex_cleaning.py

@@ -51,7 +51,7 @@ def main():
         raise FileNotFoundError
         sys.exit(3)
 
-    if group_num is not range(0, 9):
+    if group_num not in range(0, 9):
         print("group_num must be an int, between 0 and 9.")
         raise ValueError
         sys.exit(3)

Ex_contigs.py

@@ -168,8 +168,8 @@ def main():
         raise ValueError
         sys.exit(3)
 
-    if spectra is not bool:
-        print("Spectra must be boolean, True or False.")
+    if spectra not in [True, False]:
+        print("spectra must be boolean, True or False.")
         raise ValueError
         sys.exit(3)
 
@@ -202,8 +202,8 @@ def main():
         raise ValueError
         sys.exit(3)
 
-    if erp is not bool:
-        print("Spectra must be boolean, True or False.")
+    if erp not in [True, False]:
+        print("erp must be boolean, True or False.")
         raise ValueError
         sys.exit(3)
 

ML.py

@@ -158,7 +158,8 @@ def Balance(self, parentPath, filter_band="nofilter"):
             fnames = os.listdir(parentPath+"/"+folder+"/"+dataFolder)
 
             subjects = list(set(
-                [fname[:config.participantNumLen] for fname in fnames]))
+                [fname[:config.participantNumLen] for fname in fnames if
+                fname[0] == "1"]))
 
             random.shuffle(subjects)
 

config.py

@@ -41,9 +41,10 @@
 }
 
 refGroupFolders = [
-    "ref 24-30",
-    "ref 31-40",
-    "ref 41-50",
+    "CANlab",
+    # "ref 24-30",
+    # "ref 31-40",
+    # "ref 41-50",
     # "ref 51-60",
     # "ref 61-70",
     # "ref 71-80",

test_preprocessing.py

@@ -11,15 +11,10 @@
 
 class TestPreprocessing(unittest.TestCase):
 
-    def test_x(self):
-        pass
+    def test_taskdata_generation(self):
 
-    def test_raw_generation(self):
-        task = [
-            task for task in config.tasks][
-            random.randint(0, len(config.tasks)-1)]
         for sub in taskObj.subjects:
-            task_length = random.randint(1000, 10000)
+            task_length = random.randint(2000, 5000)
             eeg_file = []
             art_file = []
             evt_file = []
@@ -44,90 +39,112 @@ def test_raw_generation(self):
 
             np.savetxt(
                 taskObj.studyFolder\
-                +"/"\
-                +str(sub)\
+                +"/"+taskObj.task+"/"\
+                +sub\
                 +"_"\
-                +task\
+                +taskObj.task\
                 +"_nofilter.eeg",
                 eeg_file,
                 delimiter=" ",
                 fmt="%2.1f")
 
             np.savetxt(
                 taskObj.studyFolder\
-                +"/"\
-                +str(sub)\
+                +"/"+taskObj.task+"/"\
+                +sub\
                 +"_"\
-                +task\
+                +taskObj.task\
                 +".art",
                 art_file,
                 delimiter=" ",
                 fmt="%2.1f")
 
             np.savetxt(
                 taskObj.studyFolder\
-                +"/"\
-                +str(sub)\
+                +"/"+taskObj.task+"/"\
+                +sub\
                 +"_"\
-                +task\
+                +taskObj.task\
                 +".evt",
                 evt_file,
                 delimiter=" ",
                 fmt="%2.1f")
+
+            del eeg_file
+            del art_file
+            del evt_file
+
         self.assertEqual(
-            len(os.listdir(taskObj.studyFolder)),
+            len(os.listdir(taskObj.studyFolder+"/"+taskObj.task)),
             len(taskObj.subjects)*3)
 
-    def test_contig_generation(self):
-        length = random.randint(100, 20000)
-        art_degrees = np.linspace(0, 2, 1, endpoint=True)
-        erps = [True, False]
+    # def test_contig_generation(self):
+
+        taskObj.task_fnames = taskObj.get_task_fnames(taskObj.task)
+
+        length = random.randint(100, 2000)
+        # art_degrees = [0, 1, 2]
+        art_degrees = [1]
+        # erps = [True, False]
+        erps = [False]
+        channels = ""
+        for val in list(Signals.rand_bin_string(
+            19,
+            sample_rate=1)):
+            channels += str(val)
 
         for art_degree in art_degrees:
             for erp in erps:
                 taskObj.gen_contigs(
                     length,
-                    network_channels=Signals.rand_bin_string(
-                        19,
-                        sample_rate=1),
+                    network_channels=channels,
+                    art_degree=art_degree,
+                    erp=erp)
+                taskObj.write_contigs()
+                taskObj.gen_spectra(
+                    length,
+                    network_channels=channels,
                     art_degree=art_degree,
                     erp=erp)
 
-        assertEqual(
+        self.assertEqual(
             len(os.listdir(taskObj.studyFolder+"/contigs")),
             len(art_degrees))
 
-        assertEqual(
-            len(os.listdir(taskObj.studyFolder+"/erps")),
-            len(art_degrees))
+        # self.assertEqual(
+        #     len(os.listdir(taskObj.studyFolder+"/erps")),
+        #     len(art_degrees))
 
-        assertEqual(
+        self.assertEqual(
             len(os.listdir(taskObj.studyFolder+"/spectra")),
             len(art_degrees)*len(erps))
-            
+
 
 if __name__ == '__main__':
     # unittest.TestCase.__init__(self,x)
-    taskObj = Prep.TaskData('.')
-    taskObj.studyFolder = 'testdata/raw'
-    taskObj.task = None
-    taskObj.task_fnames = None
-
-    if not os.path.isdir(taskObj.studyFolder):
+    if not os.path.isdir('testdata/P300'):
         try:
             os.mkdir('testdata')
+            os.mkdir('testdata/P300')
         except FileExistsError:
             try:
-                os.mkdir('testdata/raw')
+                os.mkdir('testdata/P300')
             except FileExistsError:
                 print(
                     "Something went wrong creating test folders.",
-                    "Try manually deleting ''/testdata/raw'")
+                    "Try manually deleting ''/testdata/'")
                 sys.exit(1)
-    else:
-        shutil.rmtree('testdata/raw')
-        os.mkdir('testdata/raw')
 
+    taskObj = Prep.TaskData(
+        'testdata/'
+        # +  str([
+        #     task for task in config.tasks][
+        #     random.randint(0, len(config.tasks)-1)]))
+        + "P300")
+    taskObj.task_fnames = None
+    # else:
+    #     shutil.rmtree('testdata/')
+    #     os.mkdir('testdata/'+taskObj.task)
 
     # make random list of fake subjects
     # adhering to subj-number lengths defined in config.py
@@ -142,5 +159,5 @@ def test_contig_generation(self):
         while num in taskObj.subjects:
             num = random.randint(1000, 3999)
 
-        taskObj.subjects.append(num)
+        taskObj.subjects.append(str(num))
     unittest.main()