Split scans between .comm/.incomm files on export

For #21

pyzebra/__init__.py

@@ -1,6 +1,6 @@
 from pyzebra.anatric import *
 from pyzebra.ccl_findpeaks import ccl_findpeaks
-from pyzebra.ccl_io import export_comm, load_1D, parse_1D
+from pyzebra.ccl_io import export_1D, load_1D, parse_1D
 from pyzebra.fit2 import fitccl
 from pyzebra.h5 import *
 from pyzebra.merge_function import add_dict, unified_merge

pyzebra/app/panel_ccl_integrate.py

@@ -68,7 +68,10 @@ def create():
     det_data = {}
     fit_params = {}
     peak_pos_textinput_lock = False
-    js_data = ColumnDataSource(data=dict(cont=[], ext=[]))
+    js_data = {
+        ".comm": ColumnDataSource(data=dict(cont=[], ext=[])),
+        ".incomm": ColumnDataSource(data=dict(cont=[], ext=[])),
+    }
 
     def proposal_textinput_callback(_attr, _old, new):
         ccl_path = os.path.join(PROPOSAL_PATH, new.strip())
@@ -84,12 +87,7 @@ def create():
 
     def _init_datatable():
         scan_list = list(det_data["scan"].keys())
-        hkl = [
+        hkl = [f'{m["h_index"]} {m["k_index"]} {m["l_index"]}' for m in det_data["scan"].values()]
-            f'{int(m["h_index"])} {int(m["k_index"])} {int(m["l_index"])}'
-            if det_data["meta"]["indices"] == "hkl"
-            else f'{m["h_index"]} {m["k_index"]} {m["l_index"]}'
-            for m in det_data["scan"].values()
-        ]
         scan_table_source.data.update(
             scan=scan_list,
             hkl=hkl,
@@ -511,26 +509,28 @@ def create():
     preview_output_textinput = TextAreaInput(title="Export file preview:", width=500, height=400)
 
     def preview_output_button_callback():
-        if det_data["meta"]["indices"] == "hkl":
-            ext = ".comm"
-        elif det_data["meta"]["indices"] == "real":
-            ext = ".incomm"
-
         with tempfile.TemporaryDirectory() as temp_dir:
             temp_file = temp_dir + "/temp"
             export_data = deepcopy(det_data)
             for s, export in zip(scan_table_source.data["scan"], scan_table_source.data["export"]):
                 if not export:
                     del export_data["scan"][s]
-            pyzebra.export_comm(
+
+            pyzebra.export_1D(
                 export_data,
                 temp_file,
                 lorentz=lorentz_toggle.active,
                 hkl_precision=int(hkl_precision_select.value),
             )
 
-            with open(f"{temp_file}{ext}") as f:
+            exported_content = ""
-                preview_output_textinput.value = f.read()
+            for ext in (".comm", ".incomm"):
+                fname = temp_file + ext
+                if os.path.isfile(fname):
+                    with open(fname) as f:
+                        exported_content += f"{ext} file:\n" + f.read()
+
+            preview_output_textinput.value = exported_content
 
     preview_output_button = Button(label="Preview file", default_size=200)
     preview_output_button.on_click(preview_output_button_callback)
@@ -539,37 +539,29 @@ def create():
         title="hkl precision:", options=["2", "3", "4"], value="2", default_size=80
     )
 
-    def export_results(det_data):
+    def save_button_callback():
-        if det_data["meta"]["indices"] == "hkl":
-            ext = ".comm"
-        elif det_data["meta"]["indices"] == "real":
-            ext = ".incomm"
-
         with tempfile.TemporaryDirectory() as temp_dir:
             temp_file = temp_dir + "/temp"
             export_data = deepcopy(det_data)
             for s, export in zip(scan_table_source.data["scan"], scan_table_source.data["export"]):
                 if not export:
                     del export_data["scan"][s]
-            pyzebra.export_comm(
-                export_data,
-                temp_file,
-                lorentz=lorentz_toggle.active,
-                hkl_precision=int(hkl_precision_select.value),
-            )
 
-            with open(f"{temp_file}{ext}") as f:
+            pyzebra.export_1D(export_data, temp_file, lorentz=lorentz_toggle.active)
-                output_content = f.read()
 
-        return output_content, ext
+            for ext in (".comm", ".incomm"):
-
+                fname = temp_file + ext
-    def save_button_callback():
+                if os.path.isfile(fname):
-        cont, ext = export_results(det_data)
+                    with open(fname) as f:
-        js_data.data.update(cont=[cont], ext=[ext])
+                        cont = f.read()
+                else:
+                    cont = ""
+                js_data[ext].data.update(cont=[cont], ext=[ext])
 
     save_button = Button(label="Download file", button_type="success", default_size=200)
     save_button.on_click(save_button_callback)
-    save_button.js_on_click(CustomJS(args={"js_data": js_data}, code=javaScript))
+    save_button.js_on_click(CustomJS(args={"js_data": js_data[".comm"]}, code=javaScript))
+    save_button.js_on_click(CustomJS(args={"js_data": js_data[".incomm"]}, code=javaScript))
 
     findpeak_controls = column(
         row(peak_pos_textinput, column(Spacer(height=19), smooth_toggle)),

pyzebra/app/panel_param_study.py

@@ -77,7 +77,10 @@ def create():
     det_data = {}
     fit_params = {}
     peak_pos_textinput_lock = False
-    js_data = ColumnDataSource(data=dict(cont=[], ext=[]))
+    js_data = {
+        ".comm": ColumnDataSource(data=dict(cont=[], ext=[])),
+        ".incomm": ColumnDataSource(data=dict(cont=[], ext=[])),
+    }
 
     def proposal_textinput_callback(_attr, _old, new):
         full_proposal_path = os.path.join(PROPOSAL_PATH, new.strip())
@@ -612,51 +615,50 @@ def create():
     preview_output_textinput = TextAreaInput(title="Export file preview:", width=450, height=400)
 
     def preview_output_button_callback():
-        if det_data["meta"]["indices"] == "hkl":
-            ext = ".comm"
-        elif det_data["meta"]["indices"] == "real":
-            ext = ".incomm"
-
         with tempfile.TemporaryDirectory() as temp_dir:
             temp_file = temp_dir + "/temp"
             export_data = deepcopy(det_data)
             for s, export in zip(scan_table_source.data["scan"], scan_table_source.data["export"]):
                 if not export:
                     del export_data["scan"][s]
-            pyzebra.export_comm(export_data, temp_file, lorentz=lorentz_toggle.active)
 
-            with open(f"{temp_file}{ext}") as f:
+            pyzebra.export_1D(export_data, temp_file, lorentz=lorentz_toggle.active)
-                preview_output_textinput.value = f.read()
+
+            exported_content = ""
+            for ext in (".comm", ".incomm"):
+                fname = temp_file + ext
+                if os.path.isfile(fname):
+                    with open(fname) as f:
+                        exported_content += f"{ext} file:\n" + f.read()
+
+            preview_output_textinput.value = exported_content
 
     preview_output_button = Button(label="Preview file", default_size=220)
     preview_output_button.on_click(preview_output_button_callback)
 
-    def export_results(det_data):
+    def save_button_callback():
-        if det_data["meta"]["indices"] == "hkl":
-            ext = ".comm"
-        elif det_data["meta"]["indices"] == "real":
-            ext = ".incomm"
-
         with tempfile.TemporaryDirectory() as temp_dir:
             temp_file = temp_dir + "/temp"
             export_data = deepcopy(det_data)
             for s, export in zip(scan_table_source.data["scan"], scan_table_source.data["export"]):
                 if not export:
                     del export_data["scan"][s]
-            pyzebra.export_comm(export_data, temp_file, lorentz=lorentz_toggle.active)
 
-            with open(f"{temp_file}{ext}") as f:
+            pyzebra.export_1D(export_data, temp_file, lorentz=lorentz_toggle.active)
-                output_content = f.read()
 
-        return output_content, ext
+            for ext in (".comm", ".incomm"):
-
+                fname = temp_file + ext
-    def save_button_callback():
+                if os.path.isfile(fname):
-        cont, ext = export_results(det_data)
+                    with open(fname) as f:
-        js_data.data.update(cont=[cont], ext=[ext])
+                        cont = f.read()
+                else:
+                    cont = ""
+                js_data[ext].data.update(cont=[cont], ext=[ext])
 
     save_button = Button(label="Download file", button_type="success", default_size=220)
     save_button.on_click(save_button_callback)
-    save_button.js_on_click(CustomJS(args={"js_data": js_data}, code=javaScript))
+    save_button.js_on_click(CustomJS(args={"js_data": js_data[".comm"]}, code=javaScript))
+    save_button.js_on_click(CustomJS(args={"js_data": js_data[".incomm"]}, code=javaScript))
 
     findpeak_controls = column(
         row(peak_pos_textinput, column(Spacer(height=19), smooth_toggle)),

pyzebra/ccl_io.py

@@ -208,13 +208,15 @@ def parse_1D(fileobj, data_type):
         print("Unknown file extention")
 
     # utility information
-    if all(
+    metadata["indices"] = []
-        s["h_index"].is_integer() and s["k_index"].is_integer() and s["l_index"].is_integer()
+    for s in scan.values():
-        for s in scan.values()
+        if s["h_index"].is_integer() and s["k_index"].is_integer() and s["l_index"].is_integer():
-    ):
+            s["h_index"] = int(s["h_index"])
-        metadata["indices"] = "hkl"
+            s["k_index"] = int(s["k_index"])
-    else:
+            s["l_index"] = int(s["l_index"])
-        metadata["indices"] = "real"
+            metadata["indices"].append("hkl")
+        else:
+            metadata["indices"].append("real")
 
     metadata["data_type"] = data_type
     metadata["area_method"] = AREA_METHODS[0]
@@ -222,54 +224,55 @@ def parse_1D(fileobj, data_type):
     return {"meta": metadata, "scan": scan}
 
 
-def export_comm(data, path, lorentz=False, hkl_precision=2):
+def export_1D(data, path, lorentz=False, hkl_precision=2):
-    """exports data in the *.comm format
+    """Exports data in the .comm/.incomm format
-    :param lorentz: perform Lorentz correction
-    :param path: path to file + name
-    :arg data - data to export, is dict after peak fitting
 
+    Scans with integer/real hkl values are saved in .comm/.incomm files correspondingly. If no scans
+    are present for a particular output format, that file won't be created.
     """
     zebra_mode = data["meta"]["zebra_mode"]
-    if data["meta"]["indices"] == "hkl":
+    file_content = {".comm": [], ".incomm": []}
-        extension = ".comm"
-    else:  # data["meta"]["indices"] == "real":
-        extension = ".incomm"
 
-    with open(str(path + extension), "w") as out_file:
+    for (key, scan), indices in zip(data["scan"].items(), data["meta"]["indices"]):
-        for key, scan in data["scan"].items():
+        if "fit" not in scan:
-            if "fit" not in scan:
+            print("Scan skipped - no fit value for:", key)
-                print("Scan skipped - no fit value for:", key)
+            continue
-                continue
 
-            scan_str = f"{key:6}"
+        scan_str = f"{key:6}"
 
-            h, k, l = scan["h_index"], scan["k_index"], scan["l_index"]
+        h, k, l = scan["h_index"], scan["k_index"], scan["l_index"]
-            if data["meta"]["indices"] == "hkl":
+        if indices == "hkl":
-                hkl_str = f"{int(h):6}{int(k):6}{int(l):6}"
+            hkl_str = f"{h:6}{k:6}{l:6}"
-            else:  # data["meta"]["indices"] == "real"
+        else:  # indices == "real"
-                hkl_str = f"{h:8.{hkl_precision}f}{k:8.{hkl_precision}f}{l:8.{hkl_precision}f}"
+            hkl_str = f"{h:8.{hkl_precision}f}{k:8.{hkl_precision}f}{l:8.{hkl_precision}f}"
 
-            area_method = data["meta"]["area_method"]
+        area_method = data["meta"]["area_method"]
-            area_n = scan["fit"][area_method].n
+        area_n = scan["fit"][area_method].n
-            area_s = scan["fit"][area_method].s
+        area_s = scan["fit"][area_method].s
 
-            # apply lorentz correction to area
+        # apply lorentz correction to area
-            if lorentz:
+        if lorentz:
-                if zebra_mode == "bi":
+            if zebra_mode == "bi":
-                    twotheta_angle = np.deg2rad(scan["twotheta_angle"])
+                twotheta_angle = np.deg2rad(scan["twotheta_angle"])
-                    corr_factor = np.sin(twotheta_angle)
+                corr_factor = np.sin(twotheta_angle)
-                else:  # zebra_mode == "nb":
+            else:  # zebra_mode == "nb":
-                    gamma_angle = np.deg2rad(scan["gamma_angle"])
+                gamma_angle = np.deg2rad(scan["gamma_angle"])
-                    nu_angle = np.deg2rad(scan["nu_angle"])
+                nu_angle = np.deg2rad(scan["nu_angle"])
-                    corr_factor = np.sin(gamma_angle) * np.cos(nu_angle)
+                corr_factor = np.sin(gamma_angle) * np.cos(nu_angle)
 
-                area_n = np.abs(area_n * corr_factor)
+            area_n = np.abs(area_n * corr_factor)
-                area_s = np.abs(area_s * corr_factor)
+            area_s = np.abs(area_s * corr_factor)
 
-            area_str = f"{area_n:10.2f}{area_s:10.2f}"
+        area_str = f"{area_n:10.2f}{area_s:10.2f}"
 
-            ang_str = ""
+        ang_str = ""
-            for angle, _ in CCL_ANGLES[zebra_mode]:
+        for angle, _ in CCL_ANGLES[zebra_mode]:
-                ang_str = ang_str + f"{scan[angle]:8}"
+            ang_str = ang_str + f"{scan[angle]:8}"
 
-            out_file.write(scan_str + hkl_str + area_str + ang_str + "\n")
+        file_content_ref = file_content[".comm"] if indices == "hkl" else file_content[".incomm"]
+        file_content_ref.append(scan_str + hkl_str + area_str + ang_str + "\n")
+
+    for ext, content in file_content.items():
+        if content:
+            with open(path + ext, "w") as out_file:
+                out_file.writelines(content)