Add ability to load cif data

pyzebra/app/panel_ccl_prepare.py

@@ -23,6 +23,8 @@ import pyzebra
 
 
 def create():
+    cif_data = None
+
     anglim_div = Div(text="Angular min/max limits:")
     sttgamma_ti = TextInput(title="stt/gamma", width=100)
     omega_ti = TextInput(title="omega", width=100)
@@ -40,11 +42,17 @@ def create():
             phi_ti.value = " ".join(ang_lims["phi"][:2])
 
     def _update_params(params):
+        if "WAVE" in params:
             wavelen_input.value = float(params["WAVE"])
+        if "SPGR" in params:
             cryst_space_group.value = params["SPGR"]
+        if "CELL" in params:
             cryst_cell.value = params["CELL"]
+        if "UBMAT" in params:
             ub_matrix.value = " ".join(params["UBMAT"])
+        if "HLIM" in params:
             ranges_hkl.value = params["HLIM"]
+        if "SRANG" in params:
             ranges_expression.value = params["SRANG"]
 
     def open_geom_callback(_attr, _old, new):
@@ -63,8 +71,15 @@ def create():
     open_cfl = FileInput(accept=".cfl", width=200)
     open_cfl.on_change("value", open_cfl_callback)
 
+    def open_cif_callback(_attr, _old, new):
+        nonlocal cif_data
+        with io.StringIO(base64.b64decode(new).decode()) as fileobj:
+            cif_data = pyzebra.read_cif_file(fileobj)
+            _update_params(cif_data)
+
     open_cif_div = Div(text="or open CIF:")
     open_cif = FileInput(accept=".cif", width=200)
+    open_cif.on_change("value", open_cif_callback)
 
     wavelen_input = NumericInput(title="\u200B", width=70, mode="float")
 

pyzebra/sxtal_refgen.py

@@ -180,3 +180,59 @@ def read_cfl_file(fileobj):
             params[param] = val
 
     return params
+
+
+def read_cif_file(fileobj):
+    params = {"SPGR": None, "CELL": None, "ATOM": []}
+
+    cell_params = {
+        "_cell_length_a": None,
+        "_cell_length_b": None,
+        "_cell_length_c": None,
+        "_cell_angle_alpha": None,
+        "_cell_angle_beta": None,
+        "_cell_angle_gamma": None,
+    }
+    cell_param_names = tuple(cell_params)
+
+    atom_param_pos = {
+        "_atom_site_label": 0,
+        "_atom_site_type_symbol": None,
+        "_atom_site_fract_x": None,
+        "_atom_site_fract_y": None,
+        "_atom_site_fract_z": None,
+        "_atom_site_U_iso_or_equiv": None,
+        "_atom_site_occupancy": None,
+    }
+    atom_param_names = tuple(atom_param_pos)
+
+    for line in fileobj:
+        line = line.strip()
+        if line.startswith("_space_group_name_H-M_alt"):
+            _, val = line.split(maxsplit=1)
+            params["SPGR"] = val.strip("'")
+
+        elif line.startswith(cell_param_names):
+            param, val = line.split(maxsplit=1)
+            cell_params[param] = val
+
+        elif line.startswith("_atom_site_label"):  # assume this is the start of atom data
+            for ind, line in enumerate(fileobj, start=1):
+                line = line.strip()
+
+                # read fields
+                if line.startswith("_atom_site"):
+                    if line.startswith(atom_param_names):
+                        atom_param_pos[line] = ind
+                    continue
+
+                # read data till an empty line
+                if not line:
+                    break
+                vals = line.split()
+                params["ATOM"].append(" ".join([vals[ind] for ind in atom_param_pos.values()]))
+
+    if None not in cell_params.values():
+        params["CELL"] = " ".join(cell_params.values())
+
+    return params