Updating for version 0.3.2

Fix #27

.github/workflows/deployment.yaml

@@ -16,6 +16,7 @@ jobs:
       run: |
         $CONDA/bin/conda install --quiet --yes conda-build anaconda-client
         $CONDA/bin/conda config --append channels conda-forge
+        $CONDA/bin/conda config --set channel_priority strict
         $CONDA/bin/conda config --set anaconda_upload yes
 
     - name: Build and upload

pyzebra/__init__.py

@@ -4,4 +4,4 @@ from pyzebra.h5 import *
 from pyzebra.xtal import *
 from pyzebra.ccl_process import *
 
-__version__ = "0.3.1"
+__version__ = "0.3.2"

pyzebra/anatric.py

@@ -23,12 +23,13 @@ REFLECTION_PRINTER_FORMATS = [
 ALGORITHMS = ["adaptivemaxcog", "adaptivedynamic"]
 
 
-def anatric(config_file, anatric_path="/afs/psi.ch/project/sinq/rhel7/bin/anatric"):
+def anatric(config_file, anatric_path="/afs/psi.ch/project/sinq/rhel7/bin/anatric", cwd=None):
     comp_proc = subprocess.run(
         [anatric_path, config_file],
-        check=True,
         stdout=subprocess.PIPE,
         stderr=subprocess.STDOUT,
+        cwd=cwd,
+        check=True,
         text=True,
     )
     print(" ".join(comp_proc.args))
@@ -59,10 +60,13 @@ class AnatricConfig:
     def save_as(self, filename):
         self._tree.write(filename)
 
+    def tostring(self):
+        return ET.tostring(self._tree.getroot(), encoding="unicode")
+
     def _get_attr(self, name, tag, attr):
         elem = self._tree.find(name).find(tag)
         if elem is None:
-            return None
+            return ""
         return elem.attrib[attr]
 
     def _set_attr(self, name, tag, attr, value):
@@ -225,7 +229,7 @@ class AnatricConfig:
         elem = self._tree.find("crystal").find("UB")
         if elem is not None:
             return elem.text
-        return None
+        return ""
 
     @crystal_UB.setter
     def crystal_UB(self, value):
@@ -247,7 +251,7 @@ class AnatricConfig:
         elem = self._tree.find("DataFactory").find("dist1")
         if elem is not None:
             return elem.attrib["value"]
-        return None
+        return ""
 
     @dataFactory_dist1.setter
     def dataFactory_dist1(self, value):
@@ -258,7 +262,7 @@ class AnatricConfig:
         elem = self._tree.find("DataFactory").find("dist2")
         if elem is not None:
             return elem.attrib["value"]
-        return None
+        return ""
 
     @dataFactory_dist2.setter
     def dataFactory_dist2(self, value):
@@ -269,7 +273,7 @@ class AnatricConfig:
         elem = self._tree.find("DataFactory").find("dist3")
         if elem is not None:
             return elem.attrib["value"]
-        return None
+        return ""
 
     @dataFactory_dist3.setter
     def dataFactory_dist3(self, value):
@@ -310,7 +314,7 @@ class AnatricConfig:
     def _get_alg_attr(self, alg, tag, attr):
         param_elem = self._alg_elems[alg].find(tag)
         if param_elem is None:
-            return None
+            return ""
         return param_elem.attrib[attr]
 
     def _set_alg_attr(self, alg, tag, attr, value):

pyzebra/app/panel_ccl_integrate.py

@@ -47,9 +47,11 @@ from pyzebra.ccl_io import AREA_METHODS
 
 
 javaScript = """
+let j = 0;
 for (let i = 0; i < js_data.data['fname'].length; i++) {
     if (js_data.data['content'][i] === "") continue;
 
+    setTimeout(function() {
         const blob = new Blob([js_data.data['content'][i]], {type: 'text/plain'})
         const link = document.createElement('a');
         document.body.appendChild(link);
@@ -59,6 +61,9 @@ for (let i = 0; i < js_data.data['fname'].length; i++) {
         link.click();
         window.URL.revokeObjectURL(url);
         document.body.removeChild(link);
+    }, 100 * j)
+
+    j++;
 }
 """
 
@@ -72,11 +77,11 @@ def create():
         proposal = new.strip()
         year = new[:4]
         proposal_path = f"/afs/psi.ch/project/sinqdata/{year}/zebra/{proposal}"
-        ccl_file_list = []
+        file_list = []
         for file in os.listdir(proposal_path):
             if file.endswith((".ccl", ".dat")):
-                ccl_file_list.append((os.path.join(proposal_path, file), file))
+                file_list.append((os.path.join(proposal_path, file), file))
-        file_select.options = ccl_file_list
+        file_select.options = file_list
 
     proposal_textinput = TextInput(title="Proposal number:", width=210)
     proposal_textinput.on_change("value", proposal_textinput_callback)
@@ -97,11 +102,7 @@ def create():
         merge_dest_select.options = merge_options
         merge_dest_select.value = merge_options[0][0]
 
-    def ccl_file_select_callback(_attr, _old, _new):
-        pass
-
     file_select = MultiSelect(title="Available .ccl/.dat files:", width=210, height=250)
-    file_select.on_change("value", ccl_file_select_callback)
 
     def file_open_button_callback():
         nonlocal det_data
@@ -120,7 +121,6 @@ def create():
                     js_data.data.update(fname=[base + ".comm", base + ".incomm"])
 
         _init_datatable()
-        _update_preview()
 
     file_open_button = Button(label="Open New", width=100)
     file_open_button.on_click(file_open_button_callback)
@@ -156,7 +156,6 @@ def create():
                     js_data.data.update(fname=[base + ".comm", base + ".incomm"])
 
         _init_datatable()
-        _update_preview()
 
     upload_div = Div(text="or upload new .ccl/.dat files:", margin=(5, 5, 0, 5))
     upload_button = FileInput(accept=".ccl,.dat", multiple=True, width=200)
@@ -301,7 +300,12 @@ def create():
 
         _update_plot(det_data[new[0]])
 
+    def scan_table_source_callback(_attr, _old, _new):
+        _update_preview()
+
     scan_table_source = ColumnDataSource(dict(scan=[], hkl=[], fit=[], export=[]))
+    scan_table_source.on_change("data", scan_table_source_callback)
+
     scan_table = DataTable(
         source=scan_table_source,
         columns=[
@@ -425,8 +429,12 @@ def create():
         )
 
         if function == "linear":
-            fitparams["value"] = [0, 0]
+            fitparams["value"] = [0, 1]
             fitparams["vary"] = [False, True]
+            fitparams["min"] = [None, 0]
+
+        elif function == "gaussian":
+            fitparams["min"] = [0, None, None]
 
         return fitparams
 
@@ -463,7 +471,6 @@ def create():
 
         _update_plot(_get_selected_scan())
         _update_table()
-        _update_preview()
 
     fit_all_button = Button(label="Fit All", button_type="primary", width=145)
     fit_all_button.on_click(fit_all_button_callback)
@@ -476,7 +483,6 @@ def create():
 
         _update_plot(scan)
         _update_table()
-        _update_preview()
 
     fit_button = Button(label="Fit Current", width=145)
     fit_button.on_click(fit_button_callback)

pyzebra/app/panel_hdf_anatric.py

@@ -1,5 +1,6 @@
 import base64
 import io
+import os
 import re
 import tempfile
 
@@ -347,14 +348,14 @@ def create():
             temp_file = temp_dir + "/config.xml"
             config.save_as(temp_file)
             if doc.anatric_path:
-                pyzebra.anatric(temp_file, anatric_path=doc.anatric_path)
+                pyzebra.anatric(temp_file, anatric_path=doc.anatric_path, cwd=temp_dir)
             else:
-                pyzebra.anatric(temp_file)
+                pyzebra.anatric(temp_file, cwd=temp_dir)
 
-            with open(config.logfile) as f_log:
+            with open(os.path.join(temp_dir, config.logfile)) as f_log:
                 output_log.value = f_log.read()
 
-            with open(config.reflectionPrinter_file) as f_res:
+            with open(os.path.join(temp_dir, config.reflectionPrinter_file)) as f_res:
                 output_res.value = f_res.read()
 
     process_button = Button(label="Process", button_type="primary")
@@ -389,11 +390,7 @@ def create():
     )
 
     async def update_config():
-        with tempfile.TemporaryDirectory() as temp_dir:
+        output_config.value = config.tostring()
-            temp_file = temp_dir + "/config.xml"
-            config.save_as(temp_file)
-            with open(temp_file) as f_config:
-                output_config.value = f_config.read()
 
     doc.add_periodic_callback(update_config, 1000)
 

pyzebra/app/panel_hdf_viewer.py

@@ -12,9 +12,12 @@ from bokeh.models import (
     CheckboxGroup,
     ColumnDataSource,
     DataRange1d,
+    DataTable,
     Div,
     FileInput,
     Grid,
+    MultiSelect,
+    NumberFormatter,
     HoverTool,
     Image,
     Line,
@@ -27,8 +30,10 @@ from bokeh.models import (
     Rect,
     ResetTool,
     Select,
+    Slider,
     Spacer,
     Spinner,
+    TableColumn,
     TextAreaInput,
     TextInput,
     Title,
@@ -40,8 +45,8 @@ import pyzebra
 
 IMAGE_W = 256
 IMAGE_H = 128
-IMAGE_PLOT_W = int(IMAGE_W * 2.5)
+IMAGE_PLOT_W = int(IMAGE_W * 2) + 52
-IMAGE_PLOT_H = int(IMAGE_H * 2.5)
+IMAGE_PLOT_H = int(IMAGE_H * 2) + 27
 
 
 def create():
@@ -56,21 +61,19 @@ def create():
         for file in os.listdir(proposal_path):
             if file.endswith(".hdf"):
                 file_list.append((os.path.join(proposal_path, file), file))
-        filelist.options = file_list
+        file_select.options = file_list
-        filelist.value = file_list[0][0]
 
-    proposal_textinput = TextInput(title="Enter proposal number:", width=145)
+    proposal_textinput = TextInput(title="Proposal number:", width=210)
     proposal_textinput.on_change("value", proposal_textinput_callback)
 
     def upload_button_callback(_attr, _old, new):
         with io.StringIO(base64.b64decode(new).decode()) as file:
             h5meta_list = pyzebra.parse_h5meta(file)
             file_list = h5meta_list["filelist"]
-            filelist.options = [(entry, os.path.basename(entry)) for entry in file_list]
+            file_select.options = [(entry, os.path.basename(entry)) for entry in file_list]
-            filelist.value = file_list[0]
 
     upload_div = Div(text="or upload .cami file:", margin=(5, 5, 0, 5))
-    upload_button = FileInput(accept=".cami")
+    upload_button = FileInput(accept=".cami", width=200)
     upload_button.on_change("value", upload_button_callback)
 
     def update_image(index=None):
@@ -101,14 +104,14 @@ def create():
             image_glyph.color_mapper.high = im_max
 
         if "mf" in det_data:
-            mf_spinner.value = det_data["mf"][index]
+            metadata_table_source.data.update(mf=[det_data["mf"][index]])
         else:
-            mf_spinner.value = None
+            metadata_table_source.data.update(mf=[None])
 
         if "temp" in det_data:
-            temp_spinner.value = det_data["temp"][index]
+            metadata_table_source.data.update(temp=[det_data["temp"][index]])
         else:
-            temp_spinner.value = None
+            metadata_table_source.data.update(temp=[None])
 
         gamma, nu = calculate_pol(det_data, index)
         omega = np.ones((IMAGE_H, IMAGE_W)) * det_data["omega"][index]
@@ -154,30 +157,50 @@ def create():
         scanning_motor_range.reset_end = var_end
         scanning_motor_range.bounds = (var_start, var_end)
 
-    def filelist_callback(_attr, _old, new):
+    def file_select_callback(_attr, old, new):
         nonlocal det_data
-        det_data = pyzebra.read_detector_data(new)
+        if not new:
+            # skip empty selections
+            return
+
+        # Avoid selection of multiple indicies (via Shift+Click or Ctrl+Click)
+        if len(new) > 1:
+            # drop selection to the previous one
+            file_select.value = old
+            return
+
+        if len(old) > 1:
+            # skip unnecessary update caused by selection drop
+            return
+
+        det_data = pyzebra.read_detector_data(new[0])
 
         index_spinner.value = 0
         index_spinner.high = det_data["data"].shape[0] - 1
+        index_slider.end = det_data["data"].shape[0] - 1
 
         zebra_mode = det_data["zebra_mode"]
         if zebra_mode == "nb":
-            geometry_textinput.value = "normal beam"
+            metadata_table_source.data.update(geom=["normal beam"])
         else:  # zebra_mode == "bi"
-            geometry_textinput.value = "bisecting"
+            metadata_table_source.data.update(geom=["bisecting"])
 
         update_image(0)
         update_overview_plot()
 
-    filelist = Select(title="Available .hdf files:")
+    file_select = MultiSelect(title="Available .hdf files:", width=210, height=250)
-    filelist.on_change("value", filelist_callback)
+    file_select.on_change("value", file_select_callback)
 
-    def index_spinner_callback(_attr, _old, new):
+    def index_callback(_attr, _old, new):
         update_image(new)
 
-    index_spinner = Spinner(title="Image index:", value=0, low=0, width=80)
+    index_slider = Slider(value=0, start=0, end=1, show_value=False, width=400)
-    index_spinner.on_change("value", index_spinner_callback)
+
+    index_spinner = Spinner(title="Image index:", value=0, low=0, width=100)
+    index_spinner.on_change("value", index_callback)
+
+    index_slider.js_link("value_throttled", index_spinner, "value")
+    index_spinner.js_link("value", index_slider, "value")
 
     plot = Plot(
         x_range=Range1d(0, IMAGE_W, bounds=(0, IMAGE_W)),
@@ -321,7 +344,7 @@ def create():
         y_range=frame_range,
         extra_y_ranges={"scanning_motor": scanning_motor_range},
         plot_height=400,
-        plot_width=IMAGE_PLOT_W,
+        plot_width=IMAGE_PLOT_W - 3,
     )
 
     # ---- tools
@@ -359,7 +382,7 @@ def create():
         y_range=frame_range,
         extra_y_ranges={"scanning_motor": scanning_motor_range},
         plot_height=400,
-        plot_width=IMAGE_PLOT_H,
+        plot_width=IMAGE_PLOT_H + 22,
     )
 
     # ---- tools
@@ -398,7 +421,7 @@ def create():
     roi_avg_plot = Plot(
         x_range=DataRange1d(),
         y_range=DataRange1d(),
-        plot_height=200,
+        plot_height=150,
         plot_width=IMAGE_PLOT_W,
         toolbar_location="left",
     )
@@ -548,7 +571,7 @@ def create():
             int(np.ceil(frame_range.end)),
         ]
 
-        filename_id = filelist.value[-8:-4]
+        filename_id = file_select.value[0][-8:-4]
         if filename_id in roi_selection:
             roi_selection[f"{filename_id}"].append(selection)
         else:
@@ -559,11 +582,23 @@ def create():
     selection_button = Button(label="Add selection")
     selection_button.on_click(selection_button_callback)
 
-    mf_spinner = Spinner(title="Magnetic field:", format="0.00", width=100, disabled=True)
+    metadata_table_source = ColumnDataSource(dict(geom=[""], temp=[None], mf=[None]))
-    temp_spinner = Spinner(title="Temperature:", format="0.00", width=100, disabled=True)
+    num_formatter = NumberFormatter(format="0.00", nan_format="")
-    geometry_textinput = TextInput(title="Geometry:", width=120, disabled=True)
+    metadata_table = DataTable(
+        source=metadata_table_source,
+        columns=[
+            TableColumn(field="geom", title="Geometry", width=100),
+            TableColumn(field="temp", title="Temperature", formatter=num_formatter, width=100),
+            TableColumn(field="mf", title="Magnetic Field", formatter=num_formatter, width=100),
+        ],
+        width=300,
+        height=50,
+        autosize_mode="none",
+        index_position=None,
+    )
 
     # Final layout
+    import_layout = column(proposal_textinput, upload_div, upload_button, file_select)
     layout_image = column(gridplot([[proj_v, None], [plot, proj_h]], merge_tools=False))
     colormap_layout = column(
         colormap,
@@ -576,9 +611,9 @@ def create():
     layout_controls = row(
         column(selection_button, selection_list),
         Spacer(width=20),
-        column(colormap_layout),
+        column(
-        Spacer(width=20),
+            row(index_spinner, column(Spacer(height=25), index_slider)), metadata_table, hkl_button
-        column(row(mf_spinner, temp_spinner), row(geometry_textinput, index_spinner), hkl_button),
+        ),
     )
 
     layout_overview = column(
@@ -591,13 +626,8 @@ def create():
     )
 
     tab_layout = row(
-        column(
+        column(import_layout, colormap_layout),
-            row(
+        column(layout_overview, layout_controls),
-                proposal_textinput, filelist, Spacer(width=100), column(upload_div, upload_button),
-            ),
-            layout_overview,
-            layout_controls,
-        ),
         column(roi_avg_plot, layout_image),
     )
 

pyzebra/app/panel_param_study.py

@@ -81,11 +81,11 @@ def create():
         proposal = new.strip()
         year = new[:4]
         proposal_path = f"/afs/psi.ch/project/sinqdata/{year}/zebra/{proposal}"
-        dat_file_list = []
+        file_list = []
         for file in os.listdir(proposal_path):
-            if file.endswith(".dat"):
+            if file.endswith((".ccl", ".dat")):
-                dat_file_list.append((os.path.join(proposal_path, file), file))
+                file_list.append((os.path.join(proposal_path, file), file))
-        file_select.options = dat_file_list
+        file_select.options = file_list
 
     proposal_textinput = TextInput(title="Proposal number:", width=210)
     proposal_textinput.on_change("value", proposal_textinput_callback)
@@ -108,11 +108,7 @@ def create():
 
         param_select.value = "user defined"
 
-    def file_select_callback(_attr, _old, _new):
+    file_select = MultiSelect(title="Available .ccl/.dat files:", width=210, height=250)
-        pass
-
-    file_select = MultiSelect(title="Available .dat files:", width=210, height=250)
-    file_select.on_change("value", file_select_callback)
 
     def file_open_button_callback():
         nonlocal det_data
@@ -130,7 +126,6 @@ def create():
                     js_data.data.update(fname=[base + ".comm", base + ".incomm"])
 
         _init_datatable()
-        _update_preview()
 
     file_open_button = Button(label="Open New", width=100)
     file_open_button.on_click(file_open_button_callback)
@@ -165,10 +160,9 @@ def create():
                     js_data.data.update(fname=[base + ".comm", base + ".incomm"])
 
         _init_datatable()
-        _update_preview()
 
-    upload_div = Div(text="or upload new .dat files:", margin=(5, 5, 0, 5))
+    upload_div = Div(text="or upload new .ccl/.dat files:", margin=(5, 5, 0, 5))
-    upload_button = FileInput(accept=".dat", multiple=True, width=200)
+    upload_button = FileInput(accept=".ccl,.dat", multiple=True, width=200)
     upload_button.on_change("value", upload_button_callback)
 
     def append_upload_button_callback(_attr, _old, new):
@@ -183,7 +177,7 @@ def create():
         _init_datatable()
 
     append_upload_div = Div(text="append extra files:", margin=(5, 5, 0, 5))
-    append_upload_button = FileInput(accept=".dat", multiple=True, width=200)
+    append_upload_button = FileInput(accept=".ccl,.dat", multiple=True, width=200)
     append_upload_button.on_change("value", append_upload_button_callback)
 
     def monitor_spinner_callback(_attr, _old, new):
@@ -392,7 +386,12 @@ def create():
 
         _update_plot()
 
+    def scan_table_source_callback(_attr, _old, _new):
+        _update_preview()
+
     scan_table_source = ColumnDataSource(dict(file=[], scan=[], param=[], fit=[], export=[]))
+    scan_table_source.on_change("data", scan_table_source_callback)
+
     scan_table = DataTable(
         source=scan_table_source,
         columns=[
@@ -519,8 +518,12 @@ def create():
         )
 
         if function == "linear":
-            fitparams["value"] = [0, 0]
+            fitparams["value"] = [0, 1]
             fitparams["vary"] = [False, True]
+            fitparams["min"] = [None, 0]
+
+        elif function == "gaussian":
+            fitparams["min"] = [0, None, None]
 
         return fitparams
 
@@ -557,7 +560,6 @@ def create():
 
         _update_plot()
         _update_table()
-        _update_preview()
 
     fit_all_button = Button(label="Fit All", button_type="primary", width=145)
     fit_all_button.on_click(fit_all_button_callback)
@@ -570,7 +572,6 @@ def create():
 
         _update_plot()
         _update_table()
-        _update_preview()
 
     fit_button = Button(label="Fit Current", width=145)
     fit_button.on_click(fit_button_callback)

pyzebra/app/panel_spind.py

@@ -3,7 +3,6 @@ import math
 import os
 import subprocess
 import tempfile
-from collections import defaultdict
 
 import numpy as np
 from bokeh.layouts import column, row
@@ -38,6 +37,9 @@ def create():
     ub_matrices = []
 
     def process_button_callback():
+        # drop table selection to clear result fields
+        results_table_source.selected.indices = []
+
         nonlocal diff_vec
         with tempfile.TemporaryDirectory() as temp_dir:
             temp_peak_list_dir = os.path.join(temp_dir, "peak_list")
@@ -52,7 +54,7 @@ def create():
                     "-n",
                     "2",
                     "python",
-                    "spind/gen_hkl_table.py",
+                    os.path.expanduser("~/spind/gen_hkl_table.py"),
                     lattice_const_textinput.value,
                     "--max-res",
                     str(max_res_spinner.value),
@@ -79,7 +81,7 @@ def create():
                     "-n",
                     "2",
                     "python",
-                    "spind/SPIND.py",
+                    os.path.expanduser("~/spind/SPIND.py"),
                     temp_peak_list_dir,
                     temp_hkl_file,
                     "-o",
@@ -102,9 +104,11 @@ def create():
             print(comp_proc.stdout)
 
             spind_out_file = os.path.join(temp_dir, "spind.txt")
+            spind_res = dict(
+                label=[], crystal_id=[], match_rate=[], matched_peaks=[], column_5=[], ub_matrix=[],
+            )
             try:
                 with open(spind_out_file) as f_out:
-                    spind_res = defaultdict(list)
                     for line in f_out:
                         c1, c2, c3, c4, c5, *c_rest = line.split()
                         spind_res["label"].append(c1)
@@ -115,12 +119,10 @@ def create():
 
                         # last digits are spind UB matrix
                         vals = list(map(float, c_rest))
-                        ub_matrix_spind = np.array(vals).reshape(3, 3)
+                        ub_matrix_spind = np.transpose(np.array(vals).reshape(3, 3))
-                        ub_matrix = np.linalg.inv(np.transpose(ub_matrix_spind))
+                        ub_matrix = np.linalg.inv(ub_matrix_spind)
                         ub_matrices.append(ub_matrix)
-                        spind_res["ub_matrix"].append(ub_matrix_spind)
+                        spind_res["ub_matrix"].append(str(ub_matrix_spind * 1e-10))
-
-                    results_table_source.data.update(spind_res)
 
                 print(f"Content of {spind_out_file}:")
                 with open(spind_out_file) as f:
@@ -129,6 +131,8 @@ def create():
             except FileNotFoundError:
                 print("No results from spind")
 
+            results_table_source.data.update(spind_res)
+
     process_button = Button(label="Process", button_type="primary")
     process_button.on_click(process_button_callback)
 
@@ -145,10 +149,12 @@ def create():
             ub_matrix_textareainput.value = str(ub_matrix * 1e10)
             hkl_textareainput.value = res
         else:
-            ub_matrix_textareainput.value = None
+            ub_matrix_textareainput.value = ""
-            hkl_textareainput.value = None
+            hkl_textareainput.value = ""
 
-    results_table_source = ColumnDataSource(dict())
+    results_table_source = ColumnDataSource(
+        dict(label=[], crystal_id=[], match_rate=[], matched_peaks=[], column_5=[], ub_matrix=[])
+    )
     results_table = DataTable(
         source=results_table_source,
         columns=[

pyzebra/ccl_io.py

@@ -261,22 +261,24 @@ def export_1D(data, path, area_method=AREA_METHODS[0], lorentz=False, hkl_precis
         h, k, l = scan["h"], scan["k"], scan["l"]
         hkl_are_integers = isinstance(h, int)  # if True, other indices are of type 'int' too
         if hkl_are_integers:
-            hkl_str = f"{h:6}{k:6}{l:6}"
+            hkl_str = f"{h:4}{k:4}{l:4}"
         else:
             hkl_str = f"{h:8.{hkl_precision}f}{k:8.{hkl_precision}f}{l:8.{hkl_precision}f}"
 
         for name, param in scan["fit"].params.items():
             if "amplitude" in name:
+                if param.stderr is None:
+                    area_n = np.nan
+                    area_s = np.nan
+                else:
                     area_n = param.value
                     area_s = param.stderr
+                # TODO: take into account multiple peaks
                 break
         else:
-            area_n = 0
+            # no peak functions in a fit model
-            area_s = 0
+            area_n = np.nan
-
+            area_s = np.nan
-        if area_n is None or area_s is None:
-            print(f"Couldn't export scan: {scan['idx']}")
-            continue
 
         # apply lorentz correction to area
         if lorentz:

pyzebra/ccl_process.py

@@ -128,6 +128,17 @@ def fit_scan(scan, model_dict, fit_from=None, fit_to=None):
                 else:
                     param_hints[hint_name] = tmp
 
+            if "center" in param_name:
+                if np.isneginf(param_hints["min"]):
+                    param_hints["min"] = np.min(x_fit)
+
+                if np.isposinf(param_hints["max"]):
+                    param_hints["max"] = np.max(x_fit)
+
+            if "sigma" in param_name:
+                if np.isposinf(param_hints["max"]):
+                    param_hints["max"] = np.max(x_fit) - np.min(x_fit)
+
             _model.set_param_hint(param_name, **param_hints)
 
         if model is None: