[NEW] Readers: ImageStackXYZReader

pySNOM/datasets/test_xyz_read.xyz

@@ -0,0 +1,6 @@
+		225	225.818	226.636	
+0	0	36.8115	36.7974	36.7867	
+1	0	37.6639	37.6841	37.7868	
+2	0	37.4873	37.4568	34.9154	
+3	0	36.66	36.6116	36.6104	
+4	0	35.8762	35.8739	35.8703	

pySNOM/readers.py

@@ -340,3 +340,49 @@ def read(self):
             params["Scan"] = "Fourier Scan"
 
         return data, params
+
+class ImageStackXYZReader(Reader):
+    """Reads a list of images from the subfolders of the specified folder by loading the files that contain the pattern string int the filename"""
+
+    def __init__(self, fullfilepath=None):
+        super().__init__(fullfilepath)
+
+    def read(self):
+
+        if self.filename is None:
+            raise ValueError('No folder specified')
+        else:
+            with open(self.filename, encoding="utf8") as f:
+                x = next(f)  # header
+                x = x.strip()
+                x = x.split("\t")
+
+                f.seek(0)
+                next(f)
+                datacols = np.arange(2, len(x)+2)
+                C_data = np.loadtxt(f, dtype="float", usecols=datacols)
+
+                f.seek(0)
+                next(f)
+
+                metacols = np.arange(0, 2)
+                meta = np.loadtxt(
+                f,
+                dtype={"names": ('Row','Column'), "formats": (float,float)},
+                usecols=metacols,
+                )
+
+                Max_row = len(np.unique(meta["Row"]))
+                Max_col = len(np.unique(meta["Column"]))
+                Max_omega = len(x)
+
+                image_stack = []
+                for i in range(Max_omega):
+                    image_stack.append(np.reshape(C_data[:, i], (Max_col, Max_row)))
+
+                try:
+                    x = np.array([float(xi) for xi in x])
+                except ValueError:
+                    x = None
+
+                return image_stack, x

pySNOM/tests/test_readers.py

@@ -73,6 +73,15 @@ def test_legacy_nea_reader(self):
         np.testing.assert_array_equal(list(data.keys())[-1], "M")
         np.testing.assert_string_equal(params["Scan"], "Fourier Scan")
 
+    def test_xyz_reader(self):
+        f = "datasets/test_xyz_read.xyz"
+        file_reader = readers.ImageStackXYZReader(os.path.join(pySNOM.__path__[0], f))
+        data, wn = file_reader.read()
+
+        np.testing.assert_array_equal(wn, np.array([225, 225.818, 226.636]))
+        np.testing.assert_equal(np.shape(data), (3, 1, 5))
+        np.testing.assert_array_equal(data[2], [[36.7867, 37.7868, 34.9154, 36.6104, 35.8703]])
+
 
 if __name__ == "__main__":
     unittest.main()