fix pt3 test (numy 0.13)

FCS-analysis · Aug 27, 2017 · 132991c · 132991c
1 parent 8fe839b
commit 132991c
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Showing 2 changed files with 22 additions and 11 deletions.
diff --git a/pycorrfit/readfiles/read_pt3_scripts/correlation_methods.py b/pycorrfit/readfiles/read_pt3_scripts/correlation_methods.py
@@ -89,12 +89,13 @@ def tttr2xfcs (y,num,NcascStart,NcascEnd, Nsub):
                 i1,i2 = fib4.dividAndConquer(y, y+lag,y.shape[0])
 
                 #If the weights (num) are one as in the first Ncasc round, then the correlation is equal to np.sum(i1)
-                i1 = i1.astype(np.bool);
-                i2 = i2.astype(np.bool);
+                i1 = np.where(i1.astype(np.bool))[0]
+                i2 = np.where(i2.astype(np.bool))[0]
 
                 #Now we want to weight each photon corectly.
                 #Faster dot product method, faster than converting to matrix.
-                auto[(k+(j)*Nsub),:,:] = np.dot((num[i1,:]).T,num[i2,:])/delta    
+                if i1.size and i2.size:
+                    auto[(k+(j)*Nsub),:,:] = np.dot((num[i1,:]).T,num[i2,:])/delta    
 
             autotime[k+(j)*Nsub] =shift;
 
@@ -108,8 +109,9 @@ def tttr2xfcs (y,num,NcascStart,NcascEnd, Nsub):
 
 
     #Removes the trailing zeros.
-    autotime = autotime[autotime != 0]
-    auto = auto[autotime != 0,:,:]
+    idauto = np.where(autotime != 0)[0]
+    autotime = autotime[idauto]
+    auto = auto[idauto,:,:]
     return auto, autotime
 
 

diff --git a/tests/test_file_formats.py b/tests/test_file_formats.py
@@ -28,7 +28,6 @@ def test_asc_all_open():
     for f in files:
         if len([ex for ex in exclude if f.endswith(ex) ]):
             continue
-        print(f)
         dn, fn = split(f)
         data = pycorrfit.readfiles.openAny(dn, fn)
         assert len(data)
@@ -37,7 +36,6 @@ def test_asc_all_open():
 @pytest.mark.xfail(NOAPITOKEN, reason="Restrictions to GitHub API")
 def test_asc_alv7004usb():
     """Test alv7004/USB format"""
-
     f1 = data_file_dl.get_data_file("ALV-7004USB_ac01_cc01_10.ASC")
     data = pycorrfit.readfiles.openAny(f1)
     assert data["Type"] == ["AC1", "AC2", "CC12", "CC21"]
@@ -88,7 +86,6 @@ def test_csv_all_open():
     for f in files:
         if len([ex for ex in exclude if f.endswith(ex) ]):
             continue
-        print(f)
         dn, fn = split(f)
         data = pycorrfit.readfiles.openAny(dn, fn)
         assert len(data)
@@ -102,7 +99,6 @@ def test_fcs_all_open():
     for f in files:
         if len([ex for ex in exclude if f.endswith(ex) ]):
             continue
-        print(f)
         dn, fn = split(f)
         data = pycorrfit.readfiles.openAny(dn, fn)
         assert len(data)
@@ -116,12 +112,26 @@ def test_pt3_all_open():
     for f in files:
         if len([ex for ex in exclude if f.endswith(ex) ]):
             continue
-        print(f)
         dn, fn = split(f)
         data = pycorrfit.readfiles.openAny(dn, fn)
         assert len(data)
 
 
+@pytest.mark.xfail(NOAPITOKEN, reason="Restrictions to GitHub API")
+def test_pt3_basic():
+    f1 = data_file_dl.get_data_file("PicoQuant_SymphoTime32_A42F-4jul2014/Point_1.pt3")
+    data = pycorrfit.readfiles.openAny(f1)
+
+    trace = data["Trace"][0][0]
+    assert trace.shape == (600, 2)
+    assert np.allclose(trace[40], np.array([2037, 6.48]))
+
+    corr = data["Correlation"][0]
+    assert corr.shape == (150, 2)
+    assert np.allclose(corr[40], np.array([0.000698, 0.58007174877053136]))
+    assert np.allclose(corr[100], np.array([0.72089, 0.019201608388821567]))
+
+
 @pytest.mark.xfail(NOAPITOKEN, reason="Restrictions to GitHub API")
 def test_sin_all_open():
     # get list of supported file extensions
@@ -130,7 +140,6 @@ def test_sin_all_open():
     for f in files:
         if len([ex for ex in exclude if f.endswith(ex) ]):
             continue
-        print(f)
         dn, fn = split(f)
         data = pycorrfit.readfiles.openAny(dn, fn)
         assert len(data)