57 normalization good

pyproject.toml

@@ -11,7 +11,21 @@ authors = [
     {name = "Chen Zhang", email = "zhangc@ornl.gov"},
     {name = "Jean Bilheux", email = "bilheuxjm@ornl.gov"},
 ]
-dependencies = [ "numpy", "scipy", "pandas", "matplotlib", "jupyterlab", "pyyaml", "pydantic", "loguru", "nova-galaxy>=0.9.1,<0.10",
+dependencies = [
+    "numpy",
+    "scipy",
+    "pandas",
+    "astropy",
+    "matplotlib",
+    "tifffile",
+    "jupyterlab",
+    "dxchange",
+    "pyyaml",
+    "scikit-image",
+    "pydantic",
+    "loguru",
+    "nova-galaxy>=0.7.4,<0.8",
+
 ]
 
 [project.urls]
@@ -123,6 +137,9 @@ jupyterlab = ">=4.4.1,<5"
 pyyaml = ">=6.0.2,<7"
 pydantic = ">=2.11.3,<3"
 loguru = ">=0.7.2,<0.8"
+dxchange = ">=0.1.8,<0.2"
+h5py = ">=3.13.0,<4"
+tomopy = ">=1.14.4,<2"
 
 [tool.pixi.tasks]
 # PyPi packaging tasks

src/pleiades/processing/__init__.py

@@ -0,0 +1,111 @@
+PROTON_CHARGE_UNCERTAINTY = 0.005
+
+
+class Roi:
+    def __init__(self, x1=0, y1=0, x2=None, y2=None, width=None, height=None):
+        """x1 and x2 are mandatory
+        y2 or height are mandatory
+        x2 or width are mandatory"""
+
+        if x1 < 0 or y1 < 0:
+            raise ValueError("ROI top left corner coordinates must be non-negative")
+
+        if x2 is not None and width is not None:
+            raise ValueError("ROI cannot have both x2 and width defined")
+
+        if y2 is not None and height is not None:
+            raise ValueError("ROI cannot have both y2 and height defined")
+
+        if x2 is not None:
+            if x2 < 0:
+                raise ValueError("ROI x2 must be non-negative")
+
+            if x2 < x1:
+                raise ValueError("ROI x2 must be greater than or equal to x1")
+
+            if width is not None:
+                raise ValueError("ROI cannot have both x2 and width defined")
+
+        else:
+            if width is None or width <= 0:
+                raise ValueError("ROI width must be positive when x2 is not defined")
+            x2 = x1 + width
+
+        if y2 is not None:
+            if y2 < 0:
+                raise ValueError("ROI y2 must be non-negative")
+
+            if y2 < y1:
+                raise ValueError("ROI y2 must be greater than or equal to y1")
+
+            if height is not None:
+                raise ValueError("ROI cannot have both y2 and height defined")
+
+        else:
+            if height is None or height <= 0:
+                raise ValueError("ROI height must be positive when y2 is not defined")
+            y2 = y1 + height
+
+        self.x1 = x1
+        self.y1 = y1
+        self.x2 = x2
+        self.y2 = y2
+
+    def get_roi(self):
+        return (self.x1, self.y1, self.x2, self.y2)
+
+    def set_roi(self, x1, y1, x2, y2):
+        if x1 < 0 or y1 < 0 or x2 < 0 or y2 < 0:
+            raise ValueError("ROI coordinates must be non-negative")
+
+        self.x1 = x1
+        self.y1 = y1
+        self.x2 = x2
+        self.y2 = y2
+
+    def __repr__(self):
+        return f"Roi(x1={self.x1}, y1={self.y1}, x2={self.x2}, y2={self.y2})"
+
+    def __str__(self):
+        return f"Roi: (x1={self.x1}, y1={self.y1}) to (x2={self.x2}, y2={self.y2})"
+
+
+class DataType:
+    sample = "sample"
+    ob = "ob"
+    normalization = "normalization"
+
+
+class MasterDictKeys:
+    data_type = "data_type"
+    list_folders = "list_folders"
+
+    obs_data_combined = "obs_data_combined"
+    sample_data = "sample_data"
+    uncertainties_obs_data_combined = "uncertainties_obs_data_combined"
+    uncertainties_sample_data = "uncertainties_sample_data"
+
+    frame_number = "frame_number"
+    proton_charge = "proton_charge"
+    matching_ob = "matching_ob"
+    list_images = "list_images"
+    data = "data"
+    nexus_path = "nexus_path"
+    data_path = "data_path"
+    shutter_counts = "shutter_counts"
+    list_spectra = "list_spectra"
+    list_shutters = "list_shutters"
+    ext = "ext"
+
+
+class Facility:
+    ornl = "ornl"
+    lanl = "lanl"
+
+
+class NormalizationStatus:
+    all_nexus_file_found = False
+    all_spectra_file_found = False
+    all_shutter_counts_file_found = False
+    all_proton_charge_value_found = False
+    all_list_shutter_values_for_each_image_found = False