fixed inconsistency btw SPICE and Mantid conventions

scripts/rez_dispH.py

@@ -2,8 +2,8 @@
 import numpy as np
 from mpl_toolkits.axisartist import Axes
 
-from tavi.data.nxdict import NXdataset, NXentry
-from tavi.data.nxentry import NexusEntry
+from tavi.data.nexus_builder import NXdataset, NXentry
+from tavi.data.nexus_entry import NexusEntry
 from tavi.data.tavi import TAVI
 from tavi.instrument.resolution.cooper_nathans import CN
 from tavi.plotter import Plot2D

scripts/scans_rez.py

@@ -1,5 +1,5 @@
-from tavi.data.nxdict import NXdataset, NXentry
-from tavi.data.nxentry import NexusEntry
+from tavi.data.nexus_builder import NXdataset, NXentry
+from tavi.data.nexus_entry import NexusEntry
 from tavi.data.tavi import TAVI
 from tavi.instrument.resolution.cooper_nathans import CN
 from tavi.sample.xtal import Xtal

src/tavi/convert_spice_to_nexus.py

@@ -1,7 +1,7 @@
 import pathlib
 from typing import Optional
 
-from tavi.data.nxentry import NexusEntry
+from tavi.data.nexus_entry import NexusEntry
 
 
 def convert_spice_to_nexus(

src/tavi/data/nxentry.py → src/tavi/data/nexus_entry.py

@@ -5,7 +5,7 @@
 import h5py
 import numpy as np
 
-from tavi.data.nxdict import spice_data_to_nxdict
+from tavi.data.nexus_builder import spice_data_to_nxdict
 
 
 def _find_val_path(val, grp, prefix=""):

src/tavi/data/scan.py

@@ -5,7 +5,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 
-from tavi.data.nxentry import NexusEntry
+from tavi.data.nexus_entry import NexusEntry
 from tavi.data.scan_data import ScanData1D
 from tavi.plotter import Plot1D
 from tavi.sample.xtal import Xtal
@@ -97,10 +97,7 @@ def from_spice(
 
     @classmethod
     def from_nexus(cls, path_to_nexus: str, scan_num: Optional[int] = None):
-        ((name, nexus_dict),) = NexusEntry.from_nexus(
-            path_to_nexus,
-            scan_num,
-        ).items()
+        ((name, nexus_dict),) = NexusEntry.from_nexus(path_to_nexus, scan_num).items()
         return cls(name, nexus_dict)
 
     @property
@@ -122,14 +119,13 @@ def scan_info(self):
     @property
     def sample_ub_info(self):
         sample_type = self._nexus_dict.get("sample/type")
-        ub_matrix = self._nexus_dict.get("sample/orientation_matrix")
+        ub_matrix = self._nexus_dict.get("sample/orientation_matrix").reshape(3, 3)
         lattice_constants = self._nexus_dict.get("sample/unit_cell")
         if sample_type == "crystal" and (ub_matrix is not None):
             xtal = Xtal(lattice_constants)
-            (u, v) = xtal.ub_matrix_to_uv(spice_to_mantid(ub_matrix.reshape(3, 3)))
+            (u, v) = xtal.ub_matrix_to_uv(spice_to_mantid(ub_matrix))
         else:
-            u = None
-            v = None
+            (u, v) = (None, None)
 
         sample_ub_info = SampleUBInfo(
             sample_name=self._nexus_dict.get("sample/name"),
@@ -154,7 +150,7 @@ def instrument_info(self):
             analyzer=self._nexus_dict.get("analyser/type"),
             sense=(
                 self._nexus_dict.get("monochromator/sense")
-                + self._nexus_dict.get("sample/sense")
+                + self._nexus_dict.get("goniometer/sense")
                 + self._nexus_dict.get("analyser/sense")
             ),
             collimation=self._nexus_dict.get("divergence_x"),
@@ -197,7 +193,7 @@ def get_data(
         to normalize the y-axis and rebin x-axis.
 
         Args:
-            axes (x_str, y_stre): x-axis and y-axis variables
+            axes (x_str, y_str): x-axis and y-axis variables
             norm_to (norm_val (float), norm_channel(str)): value and channel for normalization
                 norm_channel should be "time", "monitor" or"mcu".
             rebin_type (str | None): "tol" or "grid"

src/tavi/data/scan_data.py

@@ -7,7 +7,7 @@
 
 
 class ScanData1D(object):
-    """1D scan data ready to be plot, with ooptions to renormalize or rebin"""
+    """1D scan data ready to be plot, with options to renormalize or rebin"""
 
     def __init__(
         self,

src/tavi/data/tavi.py

@@ -4,7 +4,7 @@
 
 import h5py
 
-from tavi.data.nxentry import NexusEntry
+from tavi.data.nexus_entry import NexusEntry
 from tavi.data.scan import Scan
 from tavi.data.scan_group import ScanGroup
 

src/tavi/instrument/components/goni.py

@@ -19,7 +19,7 @@ def __init__(
         component_name: str = "goniometer",
     ):
         self.type: str = "Y-ZX"  # Y-mZ-X for Huber stage at HB1A and HB3
-        self.sense: Literal[-1, +1] = -1
+        self.sense: Literal["-", "+"] = "-"
         self.omega_limit: Optional[tuple]
         self.sgl_limit: Optional[tuple] = (-10, 10)
         self.sgu_limit: Optional[tuple] = (-10, 10)
@@ -29,6 +29,16 @@ def __init__(
         super().__init__(param_dict)
         self.component_name = component_name
 
+    @property
+    def _sense(self):
+        match self.sense:
+            case "+":
+                return +1
+            case "-":
+                return -1
+            case _:
+                raise ValueError(f"sense {self.sense} needs to be either '+' or '-'.")
+
     @staticmethod
     def rot_x(nu):
         """rotation matrix about y-axis by angle nu

src/tavi/instrument/components/mono_ana.py

@@ -41,7 +41,7 @@ def __init__(
         self.d_spacing: float = mono_ana_xtal["PG002"]
         self.mosaic_h: float = 45.0  # horizontal mosaic, min of arc
         self.mosaic_v: float = 45.0  # vertical mosaic, if anisotropic
-        self.sense: Literal[-1, 1] = -1  # +1 for counter-clockwise, -1 for clockwise
+        self.sense: Literal["-", "+"] = "-"  # + for counter-clockwise, - for clockwise
 
         # divide by np.sqrt(12) if rectangular
         # Diameter D/4 if spherical
@@ -61,6 +61,16 @@ def __init__(
         super().__init__(param_dict, component_name)
         self.d_spacing = mono_ana_xtal[self.type]
 
+    @property
+    def _sense(self):
+        match self.sense:
+            case "+":
+                return +1
+            case "-":
+                return -1
+            case _:
+                raise ValueError(f"sense {self.sense} needs to be either '+' or '-'.")
+
     @property
     def _mosaic_h(self):
         return np.deg2rad(self.mosaic_h / 60)

src/tavi/instrument/instrument_params/cg4c.json

@@ -13,7 +13,7 @@
         "type": "PG002",
         "mosaic_h": 30,
         "mosaic_v": 30,
-        "sense": -1,
+        "sense": "-",
         "shape": "rectangular",
         "width": 7,
         "height": 15,
@@ -26,7 +26,7 @@
         "optimally_curved_v": false
     },
     "goniometer": {
-        "sense": 1,
+        "sense": "+",
         "type": "Y-ZX"
     },
     "monitor": {
@@ -37,7 +37,7 @@
         "d_spacing": 3.35416,
         "mosaic_h": 90,
         "mosaic_v": 90,
-        "sense": -1,
+        "sense": "-",
         "shape": "rectangular",
         "width": 20.0,
         "height": 18.0,