Load vendor files

src/mrsimulator/load_vendor_files.py

@@ -0,0 +1,114 @@
+# -*- coding: utf-8 -*-
+import csdmpy as cp
+import nmrglue as ng
+
+
+def load_bruker_1d(filename):
+    dic, data = ng.bruker.read(filename)
+    udic = ng.bruker.guess_udic(dic, data)
+
+    dims = list()
+    for key, value in list(udic.items()):
+        if type(key) == int:
+            obj = cp.Dimension(
+                type="linear",
+                count=value["size"],
+                increment=(str(1 / value["sw"]) + " s"),
+                coordinates_offset=(str(1 / value["car"]) + " s"),
+                origin_offset=(str(1e-6 / value["obs"]) + " s"),
+                label=value["label"],
+            )
+            dims.append(obj)
+    # dims = [cp.LinearDimension(
+    #     count=value['size'],
+    #     increment=(str(1 / value['sw']) + ' s'),
+    #     coordinates_offset=(str(1 / value['car']) + ' s'),
+    #     origin_offset=(str(1e-6 / value['obs']) + ' s'),
+    #     label=value['label'])
+    #     for key, value in list(udic.items()) if type(key) == int
+    # ]
+    csdm_data = cp.CSDM(
+        dimensions=dims, dependent_variables=[cp.as_dependent_variable(data)]
+    )
+    return csdm_data, udic
+
+
+# def plot_bruker_2d(data_2d):
+#    x = data_2d.dimensions
+#    y = data_2d.dependent_variables
+#
+#    x0 = x[0].coordinates
+#    x1 = x[1].coordinates
+#
+#    y00 = y[0].components[0]
+#
+#    si = x[0].increment
+#    extent = (
+#        (x0[0] - 0.5 * si).value,
+#        (x0[-1] + 0.5 * si).value,
+#        x1[0].value,
+#        x1[-1].value,
+#    )
+#
+#    fig, axi = plt.subplots(
+#        2, 2, gridspec_kw={"width_ratios": [4, 1], "height_ratios": [1, 4]}
+#    )
+#
+#    ax = axi[1, 0]
+#    im = NonUniformImage(ax, interpolation="nearest",
+#                         extent=extent, cmap="bone_r")
+#    im.set_data(x0, x1, y00.real / y00.real.max())
+#
+#    cbar = fig.colorbar(im)
+#    cbar.ax.set_ylabel(y[0].axis_label[0])
+#
+#    ax.images.append(im)
+#    for i in range(x1.size):
+#        ax.plot(x0, np.ones(x0.size) * x1[i], "k--", linewidth=0.5)
+#    ax.grid(axis="x", color="k", linestyle="--",
+#            linewidth=0.5, which="both")
+#
+#    ax.set_xlim([extent[0], extent[1]])
+#    ax.set_ylim([extent[2], extent[3]])
+#    ax.set_xlabel(x[0].axis_label)
+#    ax.set_ylabel(x[1].axis_label)
+#    ax.set_title(y[0].name)
+#
+#    ax0 = axi[0, 0]
+#    top = y00[-1].real
+#    ax0.plot(x0, top, "k", linewidth=0.5)
+#    ax0.set_xlim([extent[0], extent[1]])
+#    ax0.set_ylim([top.min(), top.max()])
+#    ax0.axis("off")
+#
+#    ax1 = axi[1, 1]
+#    right = y00[:, 513].real
+#    ax1.plot(right, x1, "k", linewidth=0.5)
+#    ax1.set_ylim([extent[2], extent[3]])
+#    ax1.set_xlim([right.min(), right.max()])
+#    ax1.axis("off")
+#
+#    axi[0, 1].axis("off")
+#
+#    plt.tight_layout(pad=0.0, w_pad=0.0, h_pad=0.0)
+#    plt.subplots_adjust(wspace=0.025, hspace=0.05)
+#    plt.show()
+
+
+# csdm_data, universal_dict = load_bruker_1d("ba2p2o7_zg")
+# csdm_data, universal_dict = load_bruker_1d("bruker_1d")
+
+
+# pp.pprint(universal_dict)
+# print(csdm_data)
+# plot_bruker_2d(data_2d)
+
+# ax = plt.subplot(projection="csdm")
+# ax.plot(csdm_data)
+# plt.tight_layout()
+# plt.show()
+
+
+# x = range(len(csdm_data))
+# plt.plot(csdm_data)
+# plt.show()