uupdate examples

Author: whitews

examples/compensate_example.py

@@ -2,7 +2,7 @@
 import flowutils
 import numpy
 
-fd = flowio.FlowData('example.fcs')
+fd = flowio.FlowData('fcs_files/100715.fcs')
 spill, markers = flowutils.compensate.get_spill(fd.text['spill'])
 events = numpy.reshape(fd.events, (-1, fd.channel_count))
 

examples/fabricate_fcs_file.py

@@ -3,55 +3,13 @@
 
 
 if __name__ == '__main__':
-    # these clusters have lots of overlap
-    # cluster1 = np.random.multivariate_normal(
-    #     [60000.0, 6000.0, 600.0, 6.0],
-    #     [
-    #         [2000,  100,   10,   10],
-    #         [10,   5000,   10,   10],
-    #         [10,     10, 1000,   10],
-    #         [10,     10,   10,    1]
-    #     ],
-    #     (10000,)
-    # )
-    # cluster2 = np.random.multivariate_normal(
-    #     [-100.0, -5.0, 400.0, 4000.0],
-    #     [
-    #         [10,    100,   10,   10],
-    #         [10,      5,   10,   10],
-    #         [1000,   10,   50,   10],
-    #         [10,     10,   10, 5000]
-    #     ],
-    #     (10000,)
-    # )
-    # cluster3a = np.random.multivariate_normal(
-    #     [25000, 25000.0, 25000.0, 0],
-    #     [
-    #         [1000,    0,    0,    0],
-    #         [0,    1000,    0,    0],
-    #         [0,       0, 1000,    0],
-    #         [0,       0,    0, 1000]
-    #     ],
-    #     (10000,)
-    # )
-    # cluster3b = np.random.multivariate_normal(
-    #     [25000, 0, 25000.0, 25000.0],
-    #     [
-    #         [1000,    0,    0,    0],
-    #         [0,    1000,    0,    0],
-    #         [0,       0, 1000,    0],
-    #         [0,       0,    0, 1000]
-    #     ],
-    #     (10000,)
-    # )
-
     np.random.seed(42)
 
     # these clusters are clearly separated
     cluster1 = np.random.multivariate_normal(
         [6000.0, 6000.0, 0.0, 3000.0],
         [
-            [600000,  600000,   0,   0],
+            [600000,  300,   0,   0],
             [300,   1000,   0,   0],
             [0,     0, 1,   10],
             [0,     0,   10,    1000]
@@ -113,9 +71,9 @@
     ]
 
     fh = open('data_set1.fcs', 'wb')
-    create_fcs(data_set1, channel_names, fh)
+    create_fcs(fh, data_set1, channel_names)
     fh.close()
 
     fh = open('data_set2.fcs', 'wb')
-    create_fcs(data_set2, channel_names, fh)
-    fh.close()
+    create_fcs(fh, data_set2, channel_names)
+    fh.close()

examples/print_channels.py

@@ -1,6 +1,6 @@
 import flowio
 
-fd = flowio.FlowData('data_set1.fcs')
+fd = flowio.FlowData('fcs_files/data1.fcs')
 
 print(len(fd.events))
-print(fd.text)
+print(fd.text)

examples/read_fcs_file.py

@@ -1,5 +1,7 @@
 import flowio
 import numpy
 
-f = flowio.FlowData('001_F6901PRY_21_C1_C01.fcs')
+f = flowio.FlowData('fcs_files/data1.fcs')
 n = numpy.reshape(f.events, (-1, f.channel_count))
+
+print(n.shape)