updated test data

scripts/HoV6Sn6_contour.py

@@ -1,5 +1,11 @@
 import matplotlib.pyplot as plt
+from tavi.data.spice_to_nexus import convert_spice_to_nexus
 from tavi.data.tavi import TAVI
+from tavi.plotter import Plot2DManager
+
+spice_folder = "./test_data/exp1031/"
+nexus_file_name = "./test_data/nexus_exp1031.h5"
+convert_spice_to_nexus(spice_folder, nexus_file_name)
 
 tavi = TAVI()
 
@@ -8,17 +14,57 @@
 
 nexus_file_name = "./test_data/nexus_exp1031.h5"
 tavi.load_nexus_data_from_disk(nexus_file_name)
+dataset = tavi.data["IPTS32912_HB1A_exp1031"]
 
+# -------------- 001 s1 scans ------------
+scan_list1 = [dataset[f"scan{i:04}"] for i in range(90, 121, 5)] + [dataset[f"scan{i:04}"] for i in range(127, 145, 5)]
+sg1 = tavi.generate_scan_group(
+    signals=scan_list1,
+    signal_axes=("persistent_field", "s1", "detector"),
+)
+# contour1 = sg1.generate_contour(rebin_steps=(None, 0.001), norm_channel="mcu", norm_val=1)
+contour1 = sg1.generate_contour(rebin_steps=(None, None), norm_channel="mcu", norm_val=1)
+# sg1.plot_contour(contour1, cmap="turbo", vmax=2e2, vmin=0)
 
-dataset = tavi.data["IPTS32912_HB1A_exp1031"]
+plt2d1 = Plot2DManager()
+plt2d1.zlim = [0, 5e2]
+plt2d1.title = "(0,0,1)"
+plt2d1.plot_contour(*contour1)
+
+
+# -------------- 005 s1 scans ----------
+scan_list2 = [dataset[f"scan{i:04}"] for i in range(91, 122, 5)] + [dataset[f"scan{i:04}"] for i in range(128, 144, 5)]
+sg2 = tavi.generate_scan_group(signals=scan_list2, signal_axes=("persistent_field", "s1", "detector"))
+contour2 = sg2.generate_contour(rebin_steps=(None, None), norm_channel="mcu", norm_val=1)
+# sg2.plot_contour(contour1, cmap="turbo", vmax=5e1, vmin=0)
+
+plt2d2 = Plot2DManager()
+plt2d2.zlim = [0, 5e1]
+plt2d2.title = "(0,0,5)"
+plt2d2.plot_contour(*contour2)
+
+
+# -------------- 100 s1 scans ----------
+scan_list3 = [dataset[f"scan{i:04}"] for i in range(93, 124, 5)] + [dataset[f"scan{i:04}"] for i in range(130, 145, 5)]
+sg3 = tavi.generate_scan_group(signals=scan_list3, signal_axes=("persistent_field", "s1", "detector"))
+contour3 = sg3.generate_contour(rebin_steps=(None, None), norm_channel="mcu", norm_val=1)
+# sg2.plot_contour(contour1, cmap="turbo", vmax=5e1, vmin=0)
+
+plt2d3 = Plot2DManager()
+plt2d3.zlim = [0, 8e2]
+plt2d3.title = "(1,0,0)"
+plt2d3.plot_contour(*contour3)
 
-print(len(dataset))
-# 001 s1 scans
-scan_list = [dataset[f"scan{i:04}"] for i in range(90, 121, 5)]
+# -------------- 200 s1 scans ----------
+scan_list4 = [dataset[f"scan{i:04}"] for i in range(94, 125, 5)] + [dataset[f"scan{i:04}"] for i in range(131, 145, 5)]
+sg4 = tavi.generate_scan_group(signals=scan_list4, signal_axes=("persistent_field", "s1", "detector"))
+contour4 = sg4.generate_contour(rebin_steps=(None, None), norm_channel="mcu", norm_val=1)
+# sg2.plot_contour(contour1, cmap="turbo", vmax=5e1, vmin=0)
 
-sg1 = tavi.generate_scan_group(signals=scan_list, signal_axes=("persistent_field", "s1", "detector"))
-contour1 = sg1.generate_contour(rebin_steps=(None, None))
-sg1.plot_contour(contour1, cmap="turbo")
+plt2d4 = Plot2DManager()
+plt2d4.zlim = [0, 2e2]
+plt2d4.title = "(2,0,0)"
+plt2d4.plot_contour(*contour4)
 
 
 plt.show()

scripts/test_data_conversion.py

@@ -28,8 +28,8 @@ def test_open_tavi_file(tavi):
 if __name__ == "__main__":
     tavi = TAVI()
     # test_conversion(424)
-    # test_conversion(710)
-    test_conversion(1031)
-    test_load_nexus_to_new_tavi(tavi)
+    test_conversion(710)
+    # test_conversion(1031)
+    # test_load_nexus_to_new_tavi(tavi)
 
     # test_open_exsiting_tavi()

scripts/test_fit.py

@@ -12,7 +12,7 @@ def test_fit_scan(tavi):
     curve1 = s1.generate_curve(norm_channel="mcu", norm_val=30, rebin_type="grid", rebin_step=0.25)
 
     x, y, xerr, yerr, xlabel, ylabel, title, label = curve1
-    f1 = Fit(x=x, y=y, fit_range=(0.0, 4))
+    f1 = Fit(x=x, y=y, err=yerr, fit_range=(0.0, 4))
     f1.add_background(values=(0.7,))
     f1.add_signal(
         values=(None, 3.5, None),
@@ -28,7 +28,7 @@ def test_fit_scan(tavi):
     f1.perform_fit()
 
     p1.plot_curve(*curve1)
-    p1.plot_curve(f1.x_plot, f1.y_plot, fmt="-")
+    p1.plot_curve(f1.x_plot, f1.y_plot, fmt="-", xlabel=xlabel, ylabel=ylabel, title=title)
 
     # s2 = tavi.data[datasets]["scan0043"]
     # curve2 = s2.generate_curve(norm_channel="mcu", norm_val=30, rebin_type="grid", rebin_step=0.25)

scripts/test_fit_group.py

@@ -0,0 +1,52 @@
+import matplotlib.pyplot as plt
+from tavi.data.tavi import TAVI
+from tavi.plotter import Plot1DManager, Plot2DManager
+
+
+def test_fit_group(tavi):
+    scan_list1 = [dataset[f"scan{i:04}"] for i in range(90, 121, 5)] + [
+        dataset[f"scan{i:04}"] for i in range(127, 128, 5)
+    ]
+    sg1 = tavi.generate_scan_group(signals=scan_list1, signal_axes=("persistent_field", "s1", "detector"))
+
+    # --------------- plot contour ---------------
+    contour1 = sg1.generate_contour(rebin_steps=(None, None), norm_channel="mcu", norm_val=1)
+    plt2d1 = Plot2DManager()
+    plt2d1.zlim = [0, 5e2]
+    plt2d1.title = "(0,0,1)"
+    plt2d1.plot_contour(*contour1)
+
+    # x, y, xerr, yerr, xlabel, ylabel, title, label = curve1
+    # f1 = Fit(x=x, y=y, fit_range=(0.0, 4))
+    # f1.add_background(values=(0.7,))
+    # f1.add_signal(
+    #     values=(None, 3.5, None),
+    #     vary=(True, True, True),
+    # )
+    # f1.add_signal(
+    #     model="Gaussian",
+    #     values=(None, 0, None),
+    #     vary=(True, False, True),
+    #     mins=(0, 0, 0.1),
+    #     maxs=(None, 0.1, 0.3),
+    # )
+    # f1.perform_fit()
+
+    p1 = Plot1DManager()
+    # p1.plot_curve(*curve1)
+    # p1.plot_curve(f1.x_plot, f1.y_plot, fmt="-")
+
+
+if __name__ == "__main__":
+    tavi = TAVI()
+
+    tavi_file_name = "./test_data/tavi_test_exp1031.h5"
+    tavi.new_tavi_file(tavi_file_name)
+
+    nexus_file_name = "./test_data/nexus_exp1031.h5"
+    tavi.load_nexus_data_from_disk(nexus_file_name)
+    dataset = tavi.data["IPTS32912_HB1A_exp1031"]
+
+    test_fit_group(tavi)
+
+    plt.show()

src/tavi/data/nexus_reader.py

@@ -50,6 +50,7 @@ def dataset_to_string(ds):
     num = np.size(nexus_entry["data/" + scan_info["def_x"]])
 
     data = {
+        # "Pt.": nexus_entry["sample/Pt."][...],
         "Pt.": np.arange(start=1, stop=num + 1, step=1),
         # detector
         "detector": nexus_entry["instrument/detector/data"][...],
@@ -100,20 +101,31 @@ def dataset_to_string(ds):
 
     # temprature
     temperatue_str = (
-        "coldtip",
-        "tsample",
-        "temp_a",
-        "temp_2",
-        "vti",
-        "sample",
-        "temp",
-        "dr_tsample",
-        "dr_temp",
+        (
+            "temp",
+            "temp_a",
+            "temp_2",
+            "coldtip",
+            "tsample",
+            "sample",
+        )
+        + (
+            "vti",
+            "dr_tsample",
+            "dr_temp",
+        )
+        + ("lt", "ht", "sorb_temp", "sorb", "sample_ht")
     )
     for t in nexus_entry["sample"].keys():
         if t in temperatue_str:
             data.update({t: nexus_entry["sample/" + t][...]})
 
+    # field
+    field_str = ("persistent_field",)
+    for f in nexus_entry["sample"].keys():
+        if f in field_str:
+            data.update({f: nexus_entry["sample/" + f][...]})
+
     return scan_info, sample_ub_info, instrument_info, data
 
 

src/tavi/data/scan_group.py

@@ -80,14 +80,16 @@ def generate_contour(
         # TODO problem if irregular size
         x_step, y_step = rebin_steps
         if x_step is None:
-            x_unique = np.unique(np.concatenate([np.unique(np.round(x, 1)) for x in x_array]))
-            x_diff = np.unique(np.round(np.diff(x_unique), 1))
+            x_precision = 1
+            x_unique = np.unique(np.concatenate([np.unique(np.round(x, x_precision)) for x in x_array]))
+            x_diff = np.unique(np.round(np.diff(x_unique), x_precision))
             x_diff = x_diff[x_diff > 0]
             x_step = x_diff[0]
 
         if y_step is None:
-            y_unique = np.unique(np.concatenate([np.unique(np.round(y, 1)) for y in y_array]))
-            y_diff = np.unique(np.round(np.diff(y_unique), 1))
+            y_precision = 5
+            y_unique = np.unique(np.concatenate([np.unique(np.round(y, y_precision)) for y in y_array]))
+            y_diff = np.unique(np.round(np.diff(y_unique), y_precision))
             y_diff = y_diff[y_diff > 0]
             y_step = y_diff[0]
 
@@ -124,13 +126,13 @@ def generate_contour(
 
         return (xv, yv, z, x_step, y_step, xlabel, ylabel, zlabel, title)
 
-    def plot_contour(self, contour_plot, cmap="turbo", vmax=100, ylim=None, xlim=None):
+    def plot_contour(self, contour_plot, cmap="turbo", vmax=100, vmin=0, ylim=None, xlim=None):
         """Plot contour"""
 
         x, y, z, _, _, xlabel, ylabel, zlabel, title = contour_plot
 
         fig, ax = plt.subplots()
-        p = ax.pcolormesh(x, y, z, shading="auto", cmap=cmap, vmax=vmax)
+        p = ax.pcolormesh(x, y, z, shading="auto", cmap=cmap, vmax=vmax, vmin=vmin)
         fig.colorbar(p, ax=ax)
         ax.set_title(title)
         ax.set_xlabel(xlabel)

src/tavi/plotter.py

@@ -8,7 +8,7 @@ class Plot1DManager(object):
 
     def __init__(self) -> None:
         _, self.ax = plt.subplots()
-        self.title = None
+        self.title = ""
         self.xlim = None
         self.ylim = None
         self.xlabel = None
@@ -44,7 +44,18 @@ def rez_plot_1D(self, tas, projection, hkl, en, ef, R0, axis):
         self.set_labels()
         return rez
 
-    def plot_curve(self, x, y, xerr=None, yerr=None, xlabel=None, ylabel=None, title=None, label=None, fmt="o"):
+    def plot_curve(
+        self,
+        x,
+        y,
+        xerr=None,
+        yerr=None,
+        xlabel=None,
+        ylabel=None,
+        title=None,
+        label=None,
+        fmt="o",
+    ):
         if title is not None:
             self.title = title
         if xlabel is not None:
@@ -61,10 +72,11 @@ class Plot2DManager(object):
     """Manage a plot"""
 
     def __init__(self, grid_helper=None) -> None:
-        self.fig = plt.figure(figsize=(10, 6))
+        # self.fig = plt.figure(figsize=(10, 6))
+        self.fig = plt.figure()
         self.ax = self.fig.add_subplot(111, axes_class=Axes, grid_helper=grid_helper)
 
-        self.title = None
+        self.title = ""
         self.xlim = None
         self.ylim = None
         self.zlim = None
@@ -84,7 +96,8 @@ def set_labels(self):
         self.ax.set_xlabel(self.xlabel)
         self.ax.set_ylabel(self.ylabel)
         self.ax.grid(alpha=0.6)
-        self.ax.legend()
+
+        # self.ax.legend()
 
     def plot_contour(
         self,
@@ -104,7 +117,7 @@ def plot_contour(
         self.xlabel = xlabel
         self.ylabel = ylabel
         self.zlabel = zlabel
-        self.title = title
+        self.title += title
 
         p = self.ax.pcolormesh(
             x,