script dump

generate_argand_v4.py

@@ -0,0 +1,59 @@
+import gemmi
+import numpy as np
+import matplotlib.pyplot as plt
+
+# -----------------------------
+# User input
+# -----------------------------
+mtz_file = "../data/Fext_tests_refine_5.mtz"
+F_label   = "F-model"
+PHI_label = "PHIF-model"
+n_max = 30000
+
+# -----------------------------
+# Load MTZ
+# -----------------------------
+mtz = gemmi.read_mtz_file(mtz_file)
+
+F   = np.array(mtz.column_with_label(F_label))[:n_max]
+PHI = np.array(mtz.column_with_label(PHI_label))[:n_max]
+
+# Convert to complex structure factors
+C = F * np.exp(1j * np.deg2rad(PHI))
+
+# -----------------------------
+# Head-to-tail vector plot
+# -----------------------------
+plt.figure(figsize=(7, 7))
+
+x_start, y_start = 0.0, 0.0   # first vector starts at origin
+
+for z in C:
+    dx, dy = z.real, z.imag
+
+    # draw arrow FROM (x_start, y_start) TO (x_start+dx, y_start+dy)
+    plt.arrow(
+        x_start, y_start,
+        dx, dy,
+        length_includes_head=True,
+        head_width=0.03 * abs(z),
+        alpha=0.6
+    )
+
+    # update start point for next vector
+    x_start += dx
+    y_start += dy
+
+
+
+# Mark start and end explicitly
+plt.scatter(0, 0, c="black", s=40, label="Start")
+plt.scatter(x_start, y_start, c="red", s=60, label="End")
+
+plt.xlabel("Re(F)")
+plt.ylabel("Im(F)")
+plt.title("Head-to-tail Argand plot of structure factors")
+plt.axis("equal")
+plt.grid(True)
+plt.legend()
+plt.show()