added Bi phonon data from CTAX

scripts/rez_HB1A.py

@@ -1,11 +1,30 @@
 import matplotlib.pyplot as plt
 
 from tavi.data.tavi import TAVI
+from tavi.instrument.resolution.cooper_nathans import CN
 from tavi.plotter import Plot2D
+from tavi.sample.xtal import Xtal
+
+instrument_config_json_path = "./test_data/IPTS9879_HB1A_exp978/hb1a.json"
+tas = CN(SPICE_CONVENTION=True)
+tas.load_instrument_params_from_json(instrument_config_json_path)
+
+ei = 14.450292
+ef = ei
+R0 = False
+
+sample_json_path = "./test_data/IPTS9879_HB1A_exp978/si.json"
+sample = Xtal.from_json(sample_json_path)
+tas.mount_sample(sample)
+
+rez1_l = tas.cooper_nathans(hkl_list=(1, 1, 1), ei=ei, ef=ef, R0=R0, projection=((1, 1, 0), (0, 0, 1), (1, -1, 0)))
+rez1_l.plot_ellipses()
+# rez1_q = tas.cooper_nathans(hkl_list=(0, 0, 0.5), ei=ei, ef=ef, R0=R0, projection=None)
+# ----------------------- load data ----------------------------
 
 tavi = TAVI()
 
-path_to_spice_folder = "./test_data/exp978/"
+path_to_spice_folder = "./test_data/IPTS9879_HB1A_exp978/exp978/"
 tavi.load_spice_data_from_disk(path_to_spice_folder)
 
 # -------------- Si (111) 40'-40'-40'-80' -----------------
@@ -21,7 +40,7 @@
 
 
 p1 = Plot2D()
-p1.add_contour(si_111_1, cmap="turbo", vmin=0, vmax=1.2e4)
+p1.add_contour(si_111_1, cmap="turbo", vmin=0, vmax=2.5e4)
 p1.title = sg1.name
 p1.ylim = [0.97, 1.03]
 p1.xlim = [0.97, 1.03]
@@ -44,7 +63,7 @@
 
 
 p2 = Plot2D()
-p2.add_contour(si_111_2, cmap="turbo", vmin=0, vmax=1300)
+p2.add_contour(si_111_2, cmap="turbo", vmin=0, vmax=3500)
 p2.title = sg2.name
 # p2.ylim = [0.97, 1.03]
 # p2.xlim = [0.97, 1.03]

src/tavi/data/fit.py

@@ -106,53 +106,31 @@ def add_background(
         prefix = f"b{self._num_backgrounds}_"
         self._background_models.append(Fit1D._add_model(model, prefix, nan_policy=self.nan_policy))
 
-    @staticmethod
-    def _get_param_names(models) -> list[list[str]]:
-        params = []
-        for model in models:
-            params.append(model.param_names)
-        return params
-
-    @property
-    def signal_param_names(self):
-        """Get parameter names of all signals"""
-        return Fit1D._get_param_names(self._signal_models)
-
-    @property
-    def background_param_names(self):
-        """Get parameter names of all backgrounds"""
-        return Fit1D._get_param_names(self._background_models)
+    # @staticmethod
+    # def _get_param_names(models) -> list[list[str]]:
+    #     params = []
+    #     for model in models:
+    #         params.append(model.param_names)
+    #     return params
+
+    # @property
+    # def signal_param_names(self):
+    #     """Get parameter names of all signals"""
+    #     return Fit1D._get_param_names(self._signal_models)
+
+    # @property
+    # def background_param_names(self):
+    #     """Get parameter names of all backgrounds"""
+    #     return Fit1D._get_param_names(self._background_models)
 
-    # TODO
     @property
-    def params(self) -> dict[str, dict]:
+    def params(self) -> Parameters:
         """Get fitting parameters as a dictionary with the model prefix being the key"""
 
-        all_pars = self.guess() if self._parameters is None else self._parameters
-        params_names = Fit1D._get_param_names(self._signal_models + self._background_models)
-
-        params_dict = {}
-        for names in params_names:
-            if len(names) < 1:
-                raise ValueError(f"Should have at least 1 parameter in {names}.")
-            prefix, _ = names[0].split("_")
-            param_dict = {}
-            for param_name in names:
-                param = all_pars[param_name]
-                param_dict.update(
-                    {
-                        "name": param.name,
-                        "value": param.value,
-                        "vary": param.vary,
-                        "min": param.min,
-                        "max": param.max,
-                        "expr": param.expr,
-                    }
-                )
-
-            params_dict.update({prefix: param_dict})
-
-        return params_dict
+        if self._parameters is None:
+            self._parameters = self.guess()
+
+        return self._parameters
 
     def guess(self) -> Parameters:
         """Guess fitting parameters' values
@@ -173,13 +151,18 @@ def model(self):
         compposite_model = np.sum(self._signal_models + self._background_models)
         return compposite_model
 
-    def x_to_plot(self, num_of_pts: Optional[int] = 100):
-        if num_of_pts is None:
-            x_to_plot = self.x
-        elif isinstance(num_of_pts, int):
-            x_to_plot = np.linspace(self.x.min(), self.x.max(), num=num_of_pts)
-        else:
-            raise ValueError(f"num_of_points={num_of_pts} needs to be an integer.")
+    def x_to_plot(
+        self,
+        min: Optional[float] = None,
+        max: Optional[float] = None,
+        num_of_pts: int = 100,
+    ):
+        if min is None:
+            min = self.x.min()
+        if max is None:
+            max = self.x.max()
+        x_to_plot = np.linspace(min, max, num=num_of_pts)
+
         return x_to_plot
 
     def eval(self, pars: Parameters, x: np.ndarray) -> np.ndarray:

src/tavi/plotter.py

@@ -87,6 +87,7 @@ def _add_fit_from_fitting(self, fit_data: Fit1D, num_of_pts: Optional[int] = 100
         for key, val in kwargs.items():
             data.fmt.update({key: val})
 
+    # TODO
     def add_fit(
         self, fit_data: Union[tuple[np.ndarray, np.ndarray], Fit1D], num_of_pts: Optional[int] = 100, **kwargs
     ):
@@ -98,6 +99,7 @@ def add_fit(
         else:
             raise ValueError(f"Invalid input fit_data={fit_data}")
 
+    # TODO
     def add_fit_components(self, fit_data: Fit1D, num_of_pts: Optional[int] = 100, **kwargs):
         if isinstance(fit_data, Fit1D) and (result := fit_data.result) is not None:
             x = fit_data.x_to_plot(num_of_pts)

test_data/Bi_CTAX/exp25/Calibration/index.html

@@ -0,0 +1,14 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+ <head>
+  <title>Index of /user_data/cg4c/exp25/Calibration</title>
+ </head>
+ <body>
+<h1>Index of /user_data/cg4c/exp25/Calibration</h1>
+  <table>
+   <tr><th valign="top"><img src="http://neutron.ornl.gov/icons/blank.gif" alt="[ICO]"></th><th><a href="index.html@C=N;O=D">Name</a></th><th><a href="index.html@C=M;O=A">Last modified</a></th><th><a href="index.html@C=S;O=A">Size</a></th><th><a href="index.html@C=D;O=A">Description</a></th></tr>
+   <tr><th colspan="5"><hr></th></tr>
+<tr><td valign="top"><img src="http://neutron.ornl.gov/icons/back.gif" alt="[PARENTDIR]"></td><td><a href="../index.html">Parent Directory</a>       </td><td>&nbsp;</td><td align="right">  - </td><td>&nbsp;</td></tr>
+   <tr><th colspan="5"><hr></th></tr>
+</table>
+</body></html>

test_data/Bi_CTAX/exp25/Calibration/index.html@C=D;O=A

@@ -0,0 +1,14 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+ <head>
+  <title>Index of /user_data/cg4c/exp25/Calibration</title>
+ </head>
+ <body>
+<h1>Index of /user_data/cg4c/exp25/Calibration</h1>
+  <table>
+   <tr><th valign="top"><img src="http://neutron.ornl.gov/icons/blank.gif" alt="[ICO]"></th><th><a href="index.html@C=N;O=A">Name</a></th><th><a href="index.html@C=M;O=A">Last modified</a></th><th><a href="index.html@C=S;O=A">Size</a></th><th><a href="index.html@C=D;O=D">Description</a></th></tr>
+   <tr><th colspan="5"><hr></th></tr>
+<tr><td valign="top"><img src="http://neutron.ornl.gov/icons/back.gif" alt="[PARENTDIR]"></td><td><a href="../index.html">Parent Directory</a>       </td><td>&nbsp;</td><td align="right">  - </td><td>&nbsp;</td></tr>
+   <tr><th colspan="5"><hr></th></tr>
+</table>
+</body></html>

test_data/Bi_CTAX/exp25/Calibration/index.html@C=D;O=D

@@ -0,0 +1,14 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+ <head>
+  <title>Index of /user_data/cg4c/exp25/Calibration</title>
+ </head>
+ <body>
+<h1>Index of /user_data/cg4c/exp25/Calibration</h1>
+  <table>
+   <tr><th valign="top"><img src="http://neutron.ornl.gov/icons/blank.gif" alt="[ICO]"></th><th><a href="index.html@C=N;O=A">Name</a></th><th><a href="index.html@C=M;O=A">Last modified</a></th><th><a href="index.html@C=S;O=A">Size</a></th><th><a href="index.html@C=D;O=A">Description</a></th></tr>
+   <tr><th colspan="5"><hr></th></tr>
+<tr><td valign="top"><img src="http://neutron.ornl.gov/icons/back.gif" alt="[PARENTDIR]"></td><td><a href="../index.html">Parent Directory</a>       </td><td>&nbsp;</td><td align="right">  - </td><td>&nbsp;</td></tr>
+   <tr><th colspan="5"><hr></th></tr>
+</table>
+</body></html>

test_data/Bi_CTAX/exp25/Calibration/index.html@C=M;O=A

@@ -0,0 +1,14 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+ <head>
+  <title>Index of /user_data/cg4c/exp25/Calibration</title>
+ </head>
+ <body>
+<h1>Index of /user_data/cg4c/exp25/Calibration</h1>
+  <table>
+   <tr><th valign="top"><img src="http://neutron.ornl.gov/icons/blank.gif" alt="[ICO]"></th><th><a href="index.html@C=N;O=A">Name</a></th><th><a href="index.html@C=M;O=D">Last modified</a></th><th><a href="index.html@C=S;O=A">Size</a></th><th><a href="index.html@C=D;O=A">Description</a></th></tr>
+   <tr><th colspan="5"><hr></th></tr>
+<tr><td valign="top"><img src="http://neutron.ornl.gov/icons/back.gif" alt="[PARENTDIR]"></td><td><a href="../index.html">Parent Directory</a>       </td><td>&nbsp;</td><td align="right">  - </td><td>&nbsp;</td></tr>
+   <tr><th colspan="5"><hr></th></tr>
+</table>
+</body></html>

test_data/Bi_CTAX/exp25/Calibration/index.html@C=M;O=D

@@ -0,0 +1,14 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+ <head>
+  <title>Index of /user_data/cg4c/exp25/Calibration</title>
+ </head>
+ <body>
+<h1>Index of /user_data/cg4c/exp25/Calibration</h1>
+  <table>
+   <tr><th valign="top"><img src="http://neutron.ornl.gov/icons/blank.gif" alt="[ICO]"></th><th><a href="index.html@C=N;O=A">Name</a></th><th><a href="index.html@C=M;O=A">Last modified</a></th><th><a href="index.html@C=S;O=A">Size</a></th><th><a href="index.html@C=D;O=A">Description</a></th></tr>
+   <tr><th colspan="5"><hr></th></tr>
+<tr><td valign="top"><img src="http://neutron.ornl.gov/icons/back.gif" alt="[PARENTDIR]"></td><td><a href="../index.html">Parent Directory</a>       </td><td>&nbsp;</td><td align="right">  - </td><td>&nbsp;</td></tr>
+   <tr><th colspan="5"><hr></th></tr>
+</table>
+</body></html>

test_data/Bi_CTAX/exp25/Calibration/index.html@C=N;O=A

@@ -0,0 +1,14 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+ <head>
+  <title>Index of /user_data/cg4c/exp25/Calibration</title>
+ </head>
+ <body>
+<h1>Index of /user_data/cg4c/exp25/Calibration</h1>
+  <table>
+   <tr><th valign="top"><img src="http://neutron.ornl.gov/icons/blank.gif" alt="[ICO]"></th><th><a href="index.html@C=N;O=D">Name</a></th><th><a href="index.html@C=M;O=A">Last modified</a></th><th><a href="index.html@C=S;O=A">Size</a></th><th><a href="index.html@C=D;O=A">Description</a></th></tr>
+   <tr><th colspan="5"><hr></th></tr>
+<tr><td valign="top"><img src="http://neutron.ornl.gov/icons/back.gif" alt="[PARENTDIR]"></td><td><a href="../index.html">Parent Directory</a>       </td><td>&nbsp;</td><td align="right">  - </td><td>&nbsp;</td></tr>
+   <tr><th colspan="5"><hr></th></tr>
+</table>
+</body></html>

test_data/Bi_CTAX/exp25/Calibration/index.html@C=N;O=D

@@ -0,0 +1,14 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+ <head>
+  <title>Index of /user_data/cg4c/exp25/Calibration</title>
+ </head>
+ <body>
+<h1>Index of /user_data/cg4c/exp25/Calibration</h1>
+  <table>
+   <tr><th valign="top"><img src="http://neutron.ornl.gov/icons/blank.gif" alt="[ICO]"></th><th><a href="index.html@C=N;O=A">Name</a></th><th><a href="index.html@C=M;O=A">Last modified</a></th><th><a href="index.html@C=S;O=A">Size</a></th><th><a href="index.html@C=D;O=A">Description</a></th></tr>
+   <tr><th colspan="5"><hr></th></tr>
+<tr><td valign="top"><img src="http://neutron.ornl.gov/icons/back.gif" alt="[PARENTDIR]"></td><td><a href="../index.html">Parent Directory</a>       </td><td>&nbsp;</td><td align="right">  - </td><td>&nbsp;</td></tr>
+   <tr><th colspan="5"><hr></th></tr>
+</table>
+</body></html>

test_data/Bi_CTAX/exp25/Calibration/index.html@C=S;O=A

@@ -0,0 +1,14 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+ <head>
+  <title>Index of /user_data/cg4c/exp25/Calibration</title>
+ </head>
+ <body>
+<h1>Index of /user_data/cg4c/exp25/Calibration</h1>
+  <table>
+   <tr><th valign="top"><img src="http://neutron.ornl.gov/icons/blank.gif" alt="[ICO]"></th><th><a href="index.html@C=N;O=A">Name</a></th><th><a href="index.html@C=M;O=A">Last modified</a></th><th><a href="index.html@C=S;O=D">Size</a></th><th><a href="index.html@C=D;O=A">Description</a></th></tr>
+   <tr><th colspan="5"><hr></th></tr>
+<tr><td valign="top"><img src="http://neutron.ornl.gov/icons/back.gif" alt="[PARENTDIR]"></td><td><a href="../index.html">Parent Directory</a>       </td><td>&nbsp;</td><td align="right">  - </td><td>&nbsp;</td></tr>
+   <tr><th colspan="5"><hr></th></tr>
+</table>
+</body></html>

test_data/Bi_CTAX/exp25/Calibration/index.html@C=S;O=D

@@ -0,0 +1,14 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+<html>
+ <head>
+  <title>Index of /user_data/cg4c/exp25/Calibration</title>
+ </head>
+ <body>
+<h1>Index of /user_data/cg4c/exp25/Calibration</h1>
+  <table>
+   <tr><th valign="top"><img src="http://neutron.ornl.gov/icons/blank.gif" alt="[ICO]"></th><th><a href="index.html@C=N;O=A">Name</a></th><th><a href="index.html@C=M;O=A">Last modified</a></th><th><a href="index.html@C=S;O=A">Size</a></th><th><a href="index.html@C=D;O=A">Description</a></th></tr>
+   <tr><th colspan="5"><hr></th></tr>
+<tr><td valign="top"><img src="http://neutron.ornl.gov/icons/back.gif" alt="[PARENTDIR]"></td><td><a href="../index.html">Parent Directory</a>       </td><td>&nbsp;</td><td align="right">  - </td><td>&nbsp;</td></tr>
+   <tr><th colspan="5"><hr></th></tr>
+</table>
+</body></html>