From c30edf5173823176fb1516208680d6087deb464c Mon Sep 17 00:00:00 2001
From: Gergely Nemeth <ngergihun@gmail.com>
Date: Wed, 21 May 2025 13:45:21 +0200
Subject: [PATCH 1/3] XYZ to imagestack reader

---
 pySNOM/readers.py | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/pySNOM/readers.py b/pySNOM/readers.py
index 04d14fb..f339407 100644
--- a/pySNOM/readers.py
+++ b/pySNOM/readers.py
@@ -340,3 +340,44 @@ 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)))
+
+                return image_stack, np.array(x)

From fbadbf8240dc316aedb61d8d09bbeddc14c7e5a2 Mon Sep 17 00:00:00 2001
From: Gergely Nemeth <ngergihun@gmail.com>
Date: Wed, 21 May 2025 14:44:29 +0200
Subject: [PATCH 2/3] Convert x to float

---
 pySNOM/readers.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/pySNOM/readers.py b/pySNOM/readers.py
index f339407..382b575 100644
--- a/pySNOM/readers.py
+++ b/pySNOM/readers.py
@@ -380,4 +380,9 @@ def read(self):
                 for i in range(Max_omega):
                     image_stack.append(np.reshape(C_data[:, i], (Max_col, Max_row)))
 
-                return image_stack, np.array(x)
+                try:
+                    x = np.array([float(xi) for xi in x])
+                except ValueError:
+                    x = None
+
+                return image_stack, x

From a03341d7bd5b71a0c3ca083a80fba1a94b8f5c9a Mon Sep 17 00:00:00 2001
From: Gergely Nemeth <ngergihun@gmail.com>
Date: Wed, 21 May 2025 14:44:51 +0200
Subject: [PATCH 3/3] Tests adn testdata

---
 pySNOM/datasets/test_xyz_read.xyz | 6 ++++++
 pySNOM/tests/test_readers.py      | 9 +++++++++
 2 files changed, 15 insertions(+)
 create mode 100644 pySNOM/datasets/test_xyz_read.xyz

diff --git a/pySNOM/datasets/test_xyz_read.xyz b/pySNOM/datasets/test_xyz_read.xyz
new file mode 100644
index 0000000..f8eaa32
--- /dev/null
+++ b/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	
diff --git a/pySNOM/tests/test_readers.py b/pySNOM/tests/test_readers.py
index 20e1c9d..510860a 100644
--- a/pySNOM/tests/test_readers.py
+++ b/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()