Updated MnTe scripts

scripts/HoV6Sn6_contour.py

@@ -1,8 +1,8 @@
 import matplotlib.pyplot as plt
 
-from tavi.data.plotter import Plot2DManager
 from tavi.data.scan_old.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"

scripts/MnTe_contour.py

@@ -1,148 +1,75 @@
-import matplotlib.pylab as plt
+import matplotlib.pyplot as plt
 
-from tavi.data.plotter import Plot2DManager
-from tavi.data.scan_old.spice_to_nexus import convert_spice_to_nexus
 from tavi.data.tavi import TAVI
-from tavi.instrument.resolution.cooper_nathans import CN
-from tavi.sample.xtal import Xtal
-
-spice_folder = "./test_data/exp813"
-nexus_folder = "./test_data/IPTS34735_HB3_exp0813"
-if False:
-    convert_spice_to_nexus(spice_folder, nexus_folder)
+from tavi.plotter import Plot2D
 
 tavi = TAVI()
 
-tavi_file_name = "./test_data/tavi_test_exp0813.h5"
-tavi.new(tavi_file_name)
-tavi.load_nexus_data_from_disk(nexus_folder)
-dataset = tavi.data["IPTS34735_HB3_exp0813"]
+# load two experiments from SPICE the first time
+if False:
+    tavi.load_spice_data_from_disk("./test_data/IPTS-34735/exp813/")
+    tavi.load_spice_data_from_disk("./test_data/IPTS-34735/exp823/")
+    tavi.save("./test_data/tavi_MnTe.h5")
+
+tavi.open_file("./test_data/tavi_MnTe.h5")
 
 # -------------- H0L const Q scans ------------
-scan_nums = [37, 39, 40] + list(range(44, 64)) + list(range(65, 69)) + list(range(84, 97))
-scan_list1 = [dataset[f"scan{i:04}"] for i in scan_nums]
-sg1 = tavi.generate_scan_group(
-    signals=scan_list1,
-    signal_axes=("qh", "en", "detector"),
-)
-contour1 = sg1.generate_contour(rebin_steps=(0.025, 0.25), norm_channel="mcu", norm_val=1)
-
-plt2d1 = Plot2DManager()
-plt2d1.zlim = [0, 0.5]
-plt2d1.ylim = [0, 55]
-plt2d1.title = ""
-plt2d1.plot_contour(*contour1)
-# ---------------------------------------------------------
-# resolution calculation
-# ---------------------------------------------------------
-R0 = False
-hb3 = CN()
-instrument_config_json_path = "./src/tavi/instrument/instrument_params/hb3_mnte.json"
-hb3.load_instrument_params_from_json(instrument_config_json_path)
-sample_json_path = "./test_data/test_samples/mnte.json"
-mnte = Xtal.from_json(sample_json_path)
-hb3.mount_sample(mnte)
-
-# -----------------------------------------------
-# generate  rez plot for point (1.3, 0, 1.3)
-# -----------------------------------------------
-rez_q = hb3.cooper_nathans(
-    ei=35 + 14.7,
-    ef=14.7,
-    hkl=(1.3, 0, 1.3),
-    projection=None,
-    R0=R0,
-)
-rez_q.plot()
-print(rez_q.mat)
-# -------------------------------------
-rez_hkl = hb3.cooper_nathans(
-    ei=35 + 14.7,
-    ef=14.7,
-    hkl=(1.3, 0, 1.3),
-    R0=R0,
-)
-rez_hkl.plot()
-print(rez_hkl.mat)
-# --------------------------------------
-projection = ((1, 0, 1), (-1, 2, 0), (-0.2776, 0, 0.9607))
-
-rez = hb3.cooper_nathans(
-    ei=35 + 14.7,
-    ef=14.7,
-    hkl=(1.3, 0, 1.3),
-    projection=projection,
-    R0=R0,
+# scan_list1 = [37, 39, 40] + list(range(44, 64)) + list(range(65, 69)) + list(range(84, 97))
+# sg1 = tavi.combine_scans(scan_list1, name="dispH")
+
+
+# scan_data_2d = sg1.get_data(
+#     axes=("qh", "en", "detector"),
+#     norm_to=(1, "mcu"),
+#     grid=(0.025, 0.3),
+# )
+
+# p1 = Plot2D()
+# p1.add_contour(scan_data_2d, cmap="turbo", vmax=1)
+# p1.zlim = [0, 0.5]
+# p1.ylim = [0, 50]
+# fig, ax = plt.subplots()
+# p1.plot(ax)
+
+
+# -------------- (H, 0. 2-H) Ef = 14.7 const Q scans ------------
+
+scans = list(range(88, 133))
+
+scan_list2 = [("IPTS34735_HB3_exp0823", scan) for scan in scans]
+sg2 = tavi.combine_scans(scan_list2, name="dispH (H,0,2-H) Ef=14.7 meV")
+scan_data_2 = sg2.get_data(
+    axes=("qh", "en", "detector"),
+    norm_to=(1, "mcu"),
+    grid=(0.025, 0.5),
 )
-rez.plot()
-# -----------------------------------------------
-# generate 2D rez plot
-# -----------------------------------------------
-# projection = ((1, 0, 1), (-1, 2, 0), (-1, 0, 1))
-projection = ((1, 0, 1), (-1, 2, 0), (-0.2776, 0, 0.9607))
-q1 = [1, 1.5, 0.1]  # start, stop, step
-q2 = 0
-q3 = 0
-en = [-1, 45, 5]  # start, stop, step
 
-ef = 14.7
+p2 = Plot2D()
+p2.add_contour(scan_data_2, cmap="turbo", vmin=0, vmax=1)
+p2.title = sg2.name
+p2.ylim = [0, 50]
+fig, ax = plt.subplots()
+im = p2.plot(ax)
+fig.colorbar(im)
 
-plt2d1.rez_plot(hb3, projection, q1, q2, q3, en, ef, R0)
+# -------------- (H, 0. 2-H) Ef = 30.5 meV const Q scans ------------
 
-plt.show()
+scans = list(range(133, 167))
 
-# -----------------
-# s1 = dataset["scan0045"]
-# # x, y, xerr, yerr, xlabel, ylabel, title, label
-# curve1 = s1.generate_curve(norm_channel="mcu", norm_val=1)
-# (x, y, xerr, yerr, xlabel, ylabel, title, label) = curve1
-# label += " H/L=1.15"
-# curve1 = (x, y, xerr, yerr, xlabel, ylabel, title, label)
-
-# s2 = dataset["scan0046"]
-# curve2 = s2.generate_curve(norm_channel="mcu", norm_val=1)
-# (x, y, xerr, yerr, xlabel, ylabel, title, label) = curve2
-# label += " H/L=1.20"
-# curve2 = (x, y, xerr, yerr, xlabel, ylabel, title, label)
-
-# -----------------
-# s1 = dataset["scan0049"]
-# # x, y, xerr, yerr, xlabel, ylabel, title, label
-# curve1 = s1.generate_curve(norm_channel="mcu", norm_val=1)
-# (x, y, xerr, yerr, xlabel, ylabel, title, label) = curve1
-# label += " H/L=1.3"
-# curve1 = (x, y, xerr, yerr, xlabel, ylabel, title, label)
-
-# s2 = dataset["scan0050"]
-# curve2 = s2.generate_curve(norm_channel="mcu", norm_val=1)
-# (x, y, xerr, yerr, xlabel, ylabel, title, label) = curve2
-# label += " H/L=1.3"
-# curve2 = (x, y, xerr, yerr, xlabel, ylabel, title, label)
-
-# s3 = dataset["scan0051"]
-# # x, y, xerr, yerr, xlabel, ylabel, title, label
-# curve3 = s3.generate_curve(norm_channel="mcu", norm_val=1)
-# (x, y, xerr, yerr, xlabel, ylabel, title, label) = curve3
-# label += " H/L=1.325"
-# curve3 = (x, y, xerr, yerr, xlabel, ylabel, title, label)
-
-# s4 = dataset["scan0052"]
-# curve4 = s4.generate_curve(norm_channel="mcu", norm_val=1)
-# (x, y, xerr, yerr, xlabel, ylabel, title, label) = curve4
-# label += " H/L=1.325"
-# curve4 = (x, y, xerr, yerr, xlabel, ylabel, title, label)
-
-# p1 = Plot1DManager()
-# p1.plot_curve(*curve1)
-
-# p1.plot_curve(*curve3)
-# p1.plot_curve(*curve2)
-# p1.plot_curve(*curve4)
-
-# -----------------
-# s1 = dataset["scan0062"]
-# # x, y, xerr, yerr, xlabel, ylabel, title, label
-# curve1 = s1.generate_curve(norm_channel="mcu", norm_val=1)
-# p1 = Plot1DManager()
-# p1.plot_curve(*curve1)
-# plt.show()
+scan_list3 = [("IPTS34735_HB3_exp0823", scan) for scan in scans]
+sg3 = tavi.combine_scans(scan_list3, name="dispH (H,0,2-H) Ef=30.5 meV")
+scan_data_3 = sg3.get_data(
+    axes=("qh", "en", "detector"),
+    norm_to=(1, "mcu"),
+    grid=(0.025, 0.5),
+)
+
+p3 = Plot2D()
+p3.add_contour(scan_data_3, cmap="turbo", vmin=0, vmax=1)
+p3.title = sg3.name
+p3.ylim = [0, 50]
+
+fig, ax = plt.subplots()
+im = p3.plot(ax)
+fig.colorbar(im)
+plt.show()

scripts/MnTe_lines.py

@@ -0,0 +1,32 @@
+import matplotlib.pyplot as plt
+
+from tavi.data.tavi import TAVI
+from tavi.plotter import Plot1D
+
+tavi = TAVI()
+
+# load two experiments from SPICE the first time
+if False:
+    tavi.load_spice_data_from_disk("./test_data/IPTS-34735/exp813/")
+    tavi.load_spice_data_from_disk("./test_data/IPTS-34735/exp823/")
+    tavi.save("./test_data/tavi_MnTe.h5")
+
+tavi.open_file("./test_data/tavi_MnTe.h5")
+
+
+# overplot two curves with different Ei's
+# 120,121, 145
+scan1 = [("IPTS34735_HB3_exp0823", scan) for scan in [120, 121]]
+sg4 = tavi.combine_scans(scan1, name="Ef=14.7 meV")
+l1 = sg4.get_data(norm_to=(1, "mcu"))
+
+scan2 = tavi.get_scan(("IPTS34735_HB3_exp0823", 145))
+l2 = scan2.get_data(norm_to=(1, "mcu"))
+
+p4 = Plot1D()
+p4.add_scan(l1, fmt="o")
+p4.add_scan(l2, fmt="s")
+fig, ax = plt.subplots()
+p4.plot(ax)
+
+plt.show()

scripts/rez_loader.jl

@@ -0,0 +1,9 @@
+using HDF5
+filename = "./test_data/tavi_rez.h5"
+fid = h5open(filename, "r")
+pdata = fid["processed_data"]
+scan0042 = pdata["scan0042"]
+rez_mat = read(scan0042, "rez_mat")
+
+scan0001 = fid["data"]["IPTS32124_CG4C_exp0424"]["scan0001"]
+read(scan0001["sample"], "unit_cell")

scripts/scans_rez.py

@@ -28,7 +28,7 @@
     qk_list = scan.data["qk"]
     ql_list = scan.data["ql"]
 
-    projection = ((1, 1, 0), (0, 0, 1), (1, -1, 0))
+    # projection = ((1, 1, 0), (0, 0, 1), (1, -1, 0))
     R0 = True
 
     rez_mat_list = []
@@ -40,7 +40,7 @@
             ei=ei_list[i],
             ef=ef_list[i],
             hkl=(qh_list[i], qk_list[i], ql_list[i]),
-            projection=projection,
+            # projection=projection,
             R0=R0,
         )
         rez_mat_list.append(rez.mat)
@@ -56,11 +56,11 @@
         err=NXdataset(ds=scan_data.err),
         rez_mat=NXdataset(ds=rez_mat_list),
         rez_r0=NXdataset(ds=rez_r0_list),
-        projection=NXdataset(ds=projection),
+        # projection=NXdataset(ds=projection),
     )
 
     tavi.processed_data.update(NexusEntry._dict_to_nexus_entry({scan.name: rez_entry}))
 
 
-file_path = "./test_data/tavi_rez.h5"
+file_path = "./test_data/tavi_rez_HKLE.h5"
 tavi.save(file_path)

scripts/test_fit_group.py

@@ -1,7 +1,7 @@
 import matplotlib.pyplot as plt
 
-from tavi.data.plotter import Plot1DManager, Plot2DManager
 from tavi.data.tavi import TAVI
+from tavi.plotter import Plot1DManager, Plot2DManager
 
 
 def test_fit_group(tavi):

scripts/test_plotter.py

@@ -1,8 +1,8 @@
 import matplotlib.pylab as plt
 
-from tavi.data.plotter import Plot1DManager, Plot2DManager
 from tavi.data.tavi import TAVI
 from tavi.instrument.resolution.cooper_nathans import CN
+from tavi.plotter import Plot1DManager, Plot2DManager
 
 # from tavi.instrument.instrument_params.python_dicts.cg4c import cg4c_config_params
 # from tests.test_data_folder.test_samples.python_samples.nitio3 import nitio3