Add cell volume calculation and reading of unit cell file

src/geomtools/sfx/lattice.py

@@ -2,7 +2,6 @@
 import numpy as np
 
 
-
 # Electron charge in C
 ELECTRON_CHARGE = 1.6021773e-19
 # Planck's constant (Js)
@@ -43,13 +42,58 @@ def get_min_bragg_dist(r, clen, lmd, cell):
     return min(invq / a for a in cell)
 
 
+def read_crystfel_cell(stream):
+    state = 0
+    cell = {}
+    for l in stream:
+        ln, _, _ = l.partition(';')
+        ln = ln.strip()
+        if state == 0:
+            if ln and ln.startswith("CrystFEL unit cell file"):
+                state = 1
+            elif ln:
+                raise ValueError("This is not CrystFEL unit cell file")
+        elif state == 1:
+            if ln:
+                name, _, val = ln.partition('=')
+                name = name.strip()
+                val = val.strip()
+                if name in ['a', 'b', 'c']:
+                    num, _, unit = val.partition(' ')
+                    num = float(num)
+                    if unit == 'nm':
+                        num *= 10
+                elif name in ['al', 'be', 'ga']:
+                    num, _, unit = val.partition(' ')
+                    num = float(num)
+                    if unit == 'rad':
+                        num = num / np.pi * 180
+                else:
+                    num = val
+
+                cell[name] = num
+
+    return type('UnitCell', (), cell)
+
+
+def cell_volume(a, b, c, alpha, beta, gamma):
+    al = alpha * np.pi / 180.
+    be = beta * np.pi / 180.
+    ga = gamma * np.pi / 180.
+    abc = a * b * c
+    csa, csb, csc = np.cos(al), np.cos(be), np.cos(ga)
+    V2 = abc * abc * (
+        1. - csa * csa - csb * csb - csc * csc + 2. * csa * csb * csc)
+    return np.sqrt(V2)
+
+
 def spacing(h, k, l, a, b, c, alpha, beta, gamma):
-    alpha *= np.pi / 180.
-    beta *= np.pi / 180.
-    gamma *= np.pi / 180.
+    al = alpha * np.pi / 180.
+    be = beta * np.pi / 180.
+    ga = gamma * np.pi / 180.
     a2, b2, c2, abc = a * a, b * b, c * c, a * b * c
-    sna, snb, snc = np.sin(alpha), np.sin(beta), np.sin(gamma)
-    csa, csb, csc = np.cos(alpha), np.cos(beta), np.cos(gamma)
+    sna, snb, snc = np.sin(al), np.sin(be), np.sin(ga)
+    csa, csb, csc = np.cos(al), np.cos(be), np.cos(ga)
     V2 = abc * abc * (
         1. - csa * csa - csb * csb - csc * csc + 2. * csa * csb * csc)
     S11 = b2 * c2 * sna * sna * h * h