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__ = "0.3.0"
+__version__ = "0.3.2"

pyzebra/anatric.py

@@ -23,8 +23,17 @@ REFLECTION_PRINTER_FORMATS = [
 ALGORITHMS = ["adaptivemaxcog", "adaptivedynamic"]
 
 
-def anatric(config_file, anatric_path="/afs/psi.ch/project/sinq/rhel7/bin/anatric"):
-    subprocess.run([anatric_path, config_file], check=True)
+def anatric(config_file, anatric_path="/afs/psi.ch/project/sinq/rhel7/bin/anatric", cwd=None):
+    comp_proc = subprocess.run(
+        [anatric_path, config_file],
+        stdout=subprocess.PIPE,
+        stderr=subprocess.STDOUT,
+        cwd=cwd,
+        check=True,
+        text=True,
+    )
+    print(" ".join(comp_proc.args))
+    print(comp_proc.stdout)
 
 
 class AnatricConfig:
@@ -51,10 +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):
@@ -217,7 +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):
@@ -236,12 +248,37 @@ class AnatricConfig:
 
     @property
     def dataFactory_dist1(self):
-        return self._tree.find("DataFactory").find("dist1").attrib["value"]
+        elem = self._tree.find("DataFactory").find("dist1")
+        if elem is not None:
+            return elem.attrib["value"]
+        return ""
 
     @dataFactory_dist1.setter
     def dataFactory_dist1(self, value):
         self._tree.find("DataFactory").find("dist1").attrib["value"] = value
 
+    @property
+    def dataFactory_dist2(self):
+        elem = self._tree.find("DataFactory").find("dist2")
+        if elem is not None:
+            return elem.attrib["value"]
+        return ""
+
+    @dataFactory_dist2.setter
+    def dataFactory_dist2(self, value):
+        self._tree.find("DataFactory").find("dist2").attrib["value"] = value
+
+    @property
+    def dataFactory_dist3(self):
+        elem = self._tree.find("DataFactory").find("dist3")
+        if elem is not None:
+            return elem.attrib["value"]
+        return ""
+
+    @dataFactory_dist3.setter
+    def dataFactory_dist3(self, value):
+        self._tree.find("DataFactory").find("dist3").attrib["value"] = value
+
     @property
     def reflectionPrinter_format(self):
         return self._tree.find("ReflectionPrinter").attrib["format"]
@@ -253,6 +290,14 @@ class AnatricConfig:
 
         self._tree.find("ReflectionPrinter").attrib["format"] = value
 
+    @property
+    def reflectionPrinter_file(self):
+        return self._tree.find("ReflectionPrinter").attrib["file"]
+
+    @reflectionPrinter_file.setter
+    def reflectionPrinter_file(self, value):
+        self._tree.find("ReflectionPrinter").attrib["file"] = value
+
     @property
     def algorithm(self):
         return self._tree.find("Algorithm").attrib["implementation"]
@@ -269,7 +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

@@ -10,6 +10,7 @@ from bokeh.models import (
     BasicTicker,
     Button,
     CheckboxEditor,
+    CheckboxGroup,
     ColumnDataSource,
     CustomJS,
     DataRange1d,
@@ -37,7 +38,6 @@ from bokeh.models import (
     TableColumn,
     TextAreaInput,
     TextInput,
-    Toggle,
     WheelZoomTool,
     Whisker,
 )
@@ -47,23 +47,26 @@ 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;
 
-    const blob = new Blob([js_data.data['content'][i]], {type: 'text/plain'})
-    const link = document.createElement('a');
-    document.body.appendChild(link);
-    const url = window.URL.createObjectURL(blob);
-    link.href = url;
-    link.download = js_data.data['fname'][i];
-    link.click();
-    window.URL.revokeObjectURL(url);
-    document.body.removeChild(link);
+    setTimeout(function() {
+        const blob = new Blob([js_data.data['content'][i]], {type: 'text/plain'})
+        const link = document.createElement('a');
+        document.body.appendChild(link);
+        const url = window.URL.createObjectURL(blob);
+        link.href = url;
+        link.download = js_data.data['fname'][i];
+        link.click();
+        window.URL.revokeObjectURL(url);
+        document.body.removeChild(link);
+    }, 100 * j)
+
+    j++;
 }
 """
 
-PROPOSAL_PATH = "/afs/psi.ch/project/sinqdata/2020/zebra/"
-
 
 def create():
     det_data = {}
@@ -71,14 +74,16 @@ def create():
     js_data = ColumnDataSource(data=dict(content=["", ""], fname=["", ""]))
 
     def proposal_textinput_callback(_attr, _old, new):
-        ccl_path = os.path.join(PROPOSAL_PATH, new.strip())
-        ccl_file_list = []
-        for file in os.listdir(ccl_path):
+        proposal = new.strip()
+        year = new[:4]
+        proposal_path = f"/afs/psi.ch/project/sinqdata/{year}/zebra/{proposal}"
+        file_list = []
+        for file in os.listdir(proposal_path):
             if file.endswith((".ccl", ".dat")):
-                ccl_file_list.append((os.path.join(ccl_path, file), file))
-        file_select.options = ccl_file_list
+                file_list.append((os.path.join(proposal_path, file), file))
+        file_select.options = file_list
 
-    proposal_textinput = TextInput(title="Proposal number:", default_size=145)
+    proposal_textinput = TextInput(title="Proposal number:", width=210)
     proposal_textinput.on_change("value", proposal_textinput_callback)
 
     def _init_datatable():
@@ -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:", default_size=200, height=250)
-    file_select.on_change("value", ccl_file_select_callback)
+    file_select = MultiSelect(title="Available .ccl/.dat files:", width=210, height=250)
 
     def file_open_button_callback():
         nonlocal det_data
@@ -121,7 +122,7 @@ def create():
 
         _init_datatable()
 
-    file_open_button = Button(label="Open New", default_size=100)
+    file_open_button = Button(label="Open New", width=100)
     file_open_button.on_click(file_open_button_callback)
 
     def file_append_button_callback():
@@ -135,7 +136,7 @@ def create():
 
         _init_datatable()
 
-    file_append_button = Button(label="Append", default_size=100)
+    file_append_button = Button(label="Append", width=100)
     file_append_button.on_click(file_append_button_callback)
 
     def upload_button_callback(_attr, _old, new):
@@ -157,7 +158,7 @@ def create():
         _init_datatable()
 
     upload_div = Div(text="or upload new .ccl/.dat files:", margin=(5, 5, 0, 5))
-    upload_button = FileInput(accept=".ccl,.dat", multiple=True, default_size=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):
@@ -172,7 +173,7 @@ def create():
         _init_datatable()
 
     append_upload_div = Div(text="append extra files:", margin=(5, 5, 0, 5))
-    append_upload_button = FileInput(accept=".ccl,.dat", multiple=True, default_size=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):
@@ -254,7 +255,7 @@ def create():
         plot_bkg_source, Line(x="x", y="y", line_color="green", line_dash="dashed")
     )
 
-    plot_peak_source = ColumnDataSource(dict(xs=[0], ys=[0]))
+    plot_peak_source = ColumnDataSource(dict(xs=[[0]], ys=[[0]]))
     plot_peak = plot.add_glyph(
         plot_peak_source, MultiLine(xs="xs", ys="ys", line_color="red", line_dash="dashed")
     )
@@ -299,7 +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=[
@@ -339,13 +345,13 @@ def create():
     def fit_from_spinner_callback(_attr, _old, new):
         fit_from_span.location = new
 
-    fit_from_spinner = Spinner(title="Fit from:", default_size=145)
+    fit_from_spinner = Spinner(title="Fit from:", width=145)
     fit_from_spinner.on_change("value", fit_from_spinner_callback)
 
     def fit_to_spinner_callback(_attr, _old, new):
         fit_to_span.location = new
 
-    fit_to_spinner = Spinner(title="to:", default_size=145)
+    fit_to_spinner = Spinner(title="to:", width=145)
     fit_to_spinner.on_change("value", fit_to_spinner_callback)
 
     def fitparams_add_dropdown_callback(click):
@@ -364,7 +370,7 @@ def create():
             ("Pseudo Voigt", "pvoigt"),
             # ("Pseudo Voigt1", "pseudovoigt1"),
         ],
-        default_size=145,
+        width=145,
         disabled=True,
     )
     fitparams_add_dropdown.on_click(fitparams_add_dropdown_callback)
@@ -385,7 +391,7 @@ def create():
         else:
             fitparams_table_source.data.update(dict(param=[], value=[], vary=[], min=[], max=[]))
 
-    fitparams_select = MultiSelect(options=[], height=120, default_size=145)
+    fitparams_select = MultiSelect(options=[], height=120, width=145)
     fitparams_select.tags = [0]
     fitparams_select.on_change("value", fitparams_select_callback)
 
@@ -400,7 +406,7 @@ def create():
 
             fitparams_select.value = []
 
-    fitparams_remove_button = Button(label="Remove fit function", default_size=145, disabled=True)
+    fitparams_remove_button = Button(label="Remove fit function", width=145, disabled=True)
     fitparams_remove_button.on_click(fitparams_remove_button_callback)
 
     def fitparams_factory(function):
@@ -422,6 +428,14 @@ def create():
             param=params, value=[None] * n, vary=[True] * n, min=[None] * n, max=[None] * n,
         )
 
+        if function == "linear":
+            fitparams["value"] = [0, 1]
+            fitparams["vary"] = [False, True]
+            fitparams["min"] = [None, 0]
+
+        elif function == "gaussian":
+            fitparams["min"] = [0, None, None]
+
         return fitparams
 
     fitparams_table_source = ColumnDataSource(dict(param=[], value=[], vary=[], min=[], max=[]))
@@ -458,7 +472,7 @@ def create():
         _update_plot(_get_selected_scan())
         _update_table()
 
-    fit_all_button = Button(label="Fit All", button_type="primary", default_size=145)
+    fit_all_button = Button(label="Fit All", button_type="primary", width=145)
     fit_all_button.on_click(fit_all_button_callback)
 
     def fit_button_callback():
@@ -470,22 +484,26 @@ def create():
         _update_plot(scan)
         _update_table()
 
-    fit_button = Button(label="Fit Current", default_size=145)
+    fit_button = Button(label="Fit Current", width=145)
     fit_button.on_click(fit_button_callback)
 
+    def area_method_radiobutton_callback(_handler):
+        _update_preview()
+
     area_method_radiobutton = RadioButtonGroup(
-        labels=["Fit area", "Int area"], active=0, default_size=145, disabled=True
+        labels=["Fit area", "Int area"], active=0, width=145, disabled=True
     )
+    area_method_radiobutton.on_click(area_method_radiobutton_callback)
 
-    bin_size_spinner = Spinner(
-        title="Bin size:", value=1, low=1, step=1, default_size=145, disabled=True
-    )
+    def lorentz_checkbox_callback(_handler):
+        _update_preview()
 
-    lorentz_toggle = Toggle(label="Lorentz Correction", default_size=145)
+    lorentz_checkbox = CheckboxGroup(labels=["Lorentz Correction"], width=145, margin=[13, 5, 5, 5])
+    lorentz_checkbox.on_click(lorentz_checkbox_callback)
 
-    export_preview_textinput = TextAreaInput(title="Export preview:", width=500, height=400)
+    export_preview_textinput = TextAreaInput(title="Export file preview:", width=500, height=400)
 
-    def preview_button_callback():
+    def _update_preview():
         with tempfile.TemporaryDirectory() as temp_dir:
             temp_file = temp_dir + "/temp"
             export_data = []
@@ -497,7 +515,7 @@ def create():
                 export_data,
                 temp_file,
                 area_method=AREA_METHODS[int(area_method_radiobutton.active)],
-                lorentz=lorentz_toggle.active,
+                lorentz=bool(lorentz_checkbox.active),
                 hkl_precision=int(hkl_precision_select.value),
             )
 
@@ -516,14 +534,15 @@ def create():
             js_data.data.update(content=file_content)
             export_preview_textinput.value = exported_content
 
-    preview_button = Button(label="Preview", default_size=200)
-    preview_button.on_click(preview_button_callback)
+    def hkl_precision_select_callback(_attr, _old, _new):
+        _update_preview()
 
     hkl_precision_select = Select(
-        title="hkl precision:", options=["2", "3", "4"], value="2", default_size=80
+        title="hkl precision:", options=["2", "3", "4"], value="2", width=80
     )
+    hkl_precision_select.on_change("value", hkl_precision_select_callback)
 
-    save_button = Button(label="Download preview", button_type="success", default_size=200)
+    save_button = Button(label="Download File", button_type="success", width=200)
     save_button.js_on_click(CustomJS(args={"js_data": js_data}, code=javaScript))
 
     fitpeak_controls = row(
@@ -532,8 +551,7 @@ def create():
         Spacer(width=20),
         column(
             row(fit_from_spinner, fit_to_spinner),
-            row(bin_size_spinner, column(Spacer(height=19), lorentz_toggle)),
-            row(area_method_radiobutton),
+            row(area_method_radiobutton, lorentz_checkbox),
             row(fit_button, fit_all_button),
         ),
     )
@@ -556,7 +574,7 @@ def create():
 
     export_layout = column(
         export_preview_textinput,
-        row(hkl_precision_select, column(Spacer(height=19), row(preview_button, save_button))),
+        row(hkl_precision_select, column(Spacer(height=19), row(save_button))),
     )
 
     tab_layout = column(

pyzebra/app/panel_hdf_anatric.py

@@ -1,5 +1,6 @@
 import base64
 import io
+import os
 import re
 import tempfile
 
@@ -10,9 +11,9 @@ from bokeh.models import (
     Div,
     FileInput,
     Panel,
-    RadioButtonGroup,
     Select,
     Spacer,
+    Tabs,
     TextAreaInput,
     TextInput,
 )
@@ -29,7 +30,7 @@ def create():
         config.load_from_file(file)
 
         logfile_textinput.value = config.logfile
-        logfile_verbosity_select.value = config.logfile_verbosity
+        logfile_verbosity.value = config.logfile_verbosity
 
         filelist_type.value = config.filelist_type
         filelist_format_textinput.value = config.filelist_format
@@ -44,11 +45,16 @@ def create():
         ub_textareainput.value = config.crystal_UB
 
         dataFactory_implementation_select.value = config.dataFactory_implementation
-        dataFactory_dist1_textinput.value = config.dataFactory_dist1
+        if config.dataFactory_dist1 is not None:
+            dataFactory_dist1_textinput.value = config.dataFactory_dist1
+        if config.dataFactory_dist2 is not None:
+            dataFactory_dist2_textinput.value = config.dataFactory_dist2
+        if config.dataFactory_dist3 is not None:
+            dataFactory_dist3_textinput.value = config.dataFactory_dist3
         reflectionPrinter_format_select.value = config.reflectionPrinter_format
 
-        set_active_widgets(config.algorithm)
         if config.algorithm == "adaptivemaxcog":
+            algorithm_params.active = 0
             threshold_textinput.value = config.threshold
             shell_textinput.value = config.shell
             steepness_textinput.value = config.steepness
@@ -57,6 +63,7 @@ def create():
             aps_window_textinput.value = str(tuple(map(int, config.aps_window.values())))
 
         elif config.algorithm == "adaptivedynamic":
+            algorithm_params.active = 1
             adm_window_textinput.value = str(tuple(map(int, config.adm_window.values())))
             border_textinput.value = str(tuple(map(int, config.border.values())))
             minWindow_textinput.value = str(tuple(map(int, config.minWindow.values())))
@@ -66,45 +73,16 @@ def create():
             loop_textinput.value = config.loop
             minPeakCount_textinput.value = config.minPeakCount
             displacementCurve_textinput.value = "\n".join(map(str, config.displacementCurve))
+
         else:
             raise ValueError("Unknown processing mode.")
 
-    def set_active_widgets(implementation):
-        if implementation == "adaptivemaxcog":
-            mode_radio_button_group.active = 0
-            disable_adaptivemaxcog = False
-            disable_adaptivedynamic = True
-
-        elif implementation == "adaptivedynamic":
-            mode_radio_button_group.active = 1
-            disable_adaptivemaxcog = True
-            disable_adaptivedynamic = False
-        else:
-            raise ValueError("Implementation can be either 'adaptivemaxcog' or 'adaptivedynamic'")
-
-        threshold_textinput.disabled = disable_adaptivemaxcog
-        shell_textinput.disabled = disable_adaptivemaxcog
-        steepness_textinput.disabled = disable_adaptivemaxcog
-        duplicateDistance_textinput.disabled = disable_adaptivemaxcog
-        maxequal_textinput.disabled = disable_adaptivemaxcog
-        aps_window_textinput.disabled = disable_adaptivemaxcog
-
-        adm_window_textinput.disabled = disable_adaptivedynamic
-        border_textinput.disabled = disable_adaptivedynamic
-        minWindow_textinput.disabled = disable_adaptivedynamic
-        reflectionFile_textinput.disabled = disable_adaptivedynamic
-        targetMonitor_textinput.disabled = disable_adaptivedynamic
-        smoothSize_textinput.disabled = disable_adaptivedynamic
-        loop_textinput.disabled = disable_adaptivedynamic
-        minPeakCount_textinput.disabled = disable_adaptivedynamic
-        displacementCurve_textinput.disabled = disable_adaptivedynamic
-
     def upload_button_callback(_attr, _old, new):
         with io.BytesIO(base64.b64decode(new)) as file:
             _load_config_file(file)
 
-    upload_div = Div(text="Open XML configuration file:")
-    upload_button = FileInput(accept=".xml")
+    upload_div = Div(text="Open .xml config:")
+    upload_button = FileInput(accept=".xml", width=200)
     upload_button.on_change("value", upload_button_callback)
 
     # General parameters
@@ -112,16 +90,14 @@ def create():
     def logfile_textinput_callback(_attr, _old, new):
         config.logfile = new
 
-    logfile_textinput = TextInput(title="Logfile:", value="logfile.log", width=320)
+    logfile_textinput = TextInput(title="Logfile:", value="logfile.log")
     logfile_textinput.on_change("value", logfile_textinput_callback)
 
-    def logfile_verbosity_select_callback(_attr, _old, new):
+    def logfile_verbosity_callback(_attr, _old, new):
         config.logfile_verbosity = new
 
-    logfile_verbosity_select = Select(
-        title="verbosity:", options=["0", "5", "10", "15", "30"], width=70
-    )
-    logfile_verbosity_select.on_change("value", logfile_verbosity_select_callback)
+    logfile_verbosity = TextInput(title="verbosity:", width=70)
+    logfile_verbosity.on_change("value", logfile_verbosity_callback)
 
     # ---- FileList
     def filelist_type_callback(_attr, _old, new):
@@ -148,20 +124,20 @@ def create():
             ranges.append(re.findall(r"\b\d+\b", line))
         config.filelist_ranges = ranges
 
-    filelist_ranges_textareainput = TextAreaInput(title="ranges:", height=100)
+    filelist_ranges_textareainput = TextAreaInput(title="ranges:", rows=1)
     filelist_ranges_textareainput.on_change("value", filelist_ranges_textareainput_callback)
 
     # ---- crystal
     def crystal_sample_textinput_callback(_attr, _old, new):
         config.crystal_sample = new
 
-    crystal_sample_textinput = TextInput(title="Sample Name:")
+    crystal_sample_textinput = TextInput(title="Sample Name:", width=290)
     crystal_sample_textinput.on_change("value", crystal_sample_textinput_callback)
 
     def lambda_textinput_callback(_attr, _old, new):
         config.crystal_lambda = new
 
-    lambda_textinput = TextInput(title="lambda:", width=145)
+    lambda_textinput = TextInput(title="lambda:", width=100)
     lambda_textinput.on_change("value", lambda_textinput_callback)
 
     def ub_textareainput_callback(_attr, _old, new):
@@ -173,19 +149,19 @@ def create():
     def zeroOM_textinput_callback(_attr, _old, new):
         config.crystal_zeroOM = new
 
-    zeroOM_textinput = TextInput(title="zeroOM:", width=145)
+    zeroOM_textinput = TextInput(title="zeroOM:", width=100)
     zeroOM_textinput.on_change("value", zeroOM_textinput_callback)
 
     def zeroSTT_textinput_callback(_attr, _old, new):
         config.crystal_zeroSTT = new
 
-    zeroSTT_textinput = TextInput(title="zeroSTT:", width=145)
+    zeroSTT_textinput = TextInput(title="zeroSTT:", width=100)
     zeroSTT_textinput.on_change("value", zeroSTT_textinput_callback)
 
     def zeroCHI_textinput_callback(_attr, _old, new):
         config.crystal_zeroCHI = new
 
-    zeroCHI_textinput = TextInput(title="zeroCHI:", width=145)
+    zeroCHI_textinput = TextInput(title="zeroCHI:", width=100)
     zeroCHI_textinput.on_change("value", zeroCHI_textinput_callback)
 
     # ---- DataFactory
@@ -200,9 +176,21 @@ def create():
     def dataFactory_dist1_textinput_callback(_attr, _old, new):
         config.dataFactory_dist1 = new
 
-    dataFactory_dist1_textinput = TextInput(title="dist1:", width=145)
+    dataFactory_dist1_textinput = TextInput(title="dist1:", width=75)
     dataFactory_dist1_textinput.on_change("value", dataFactory_dist1_textinput_callback)
 
+    def dataFactory_dist2_textinput_callback(_attr, _old, new):
+        config.dataFactory_dist2 = new
+
+    dataFactory_dist2_textinput = TextInput(title="dist2:", width=75)
+    dataFactory_dist2_textinput.on_change("value", dataFactory_dist2_textinput_callback)
+
+    def dataFactory_dist3_textinput_callback(_attr, _old, new):
+        config.dataFactory_dist3 = new
+
+    dataFactory_dist3_textinput = TextInput(title="dist3:", width=75)
+    dataFactory_dist3_textinput.on_change("value", dataFactory_dist3_textinput_callback)
+
     # ---- BackgroundProcessor
 
     # ---- DetectorEfficency
@@ -221,42 +209,42 @@ def create():
     def threshold_textinput_callback(_attr, _old, new):
         config.threshold = new
 
-    threshold_textinput = TextInput(title="Threshold:")
+    threshold_textinput = TextInput(title="Threshold:", width=145)
     threshold_textinput.on_change("value", threshold_textinput_callback)
 
     # ---- shell
     def shell_textinput_callback(_attr, _old, new):
         config.shell = new
 
-    shell_textinput = TextInput(title="Shell:")
+    shell_textinput = TextInput(title="Shell:", width=145)
     shell_textinput.on_change("value", shell_textinput_callback)
 
     # ---- steepness
     def steepness_textinput_callback(_attr, _old, new):
         config.steepness = new
 
-    steepness_textinput = TextInput(title="Steepness:")
+    steepness_textinput = TextInput(title="Steepness:", width=145)
     steepness_textinput.on_change("value", steepness_textinput_callback)
 
     # ---- duplicateDistance
     def duplicateDistance_textinput_callback(_attr, _old, new):
         config.duplicateDistance = new
 
-    duplicateDistance_textinput = TextInput(title="Duplicate Distance:")
+    duplicateDistance_textinput = TextInput(title="Duplicate Distance:", width=145)
     duplicateDistance_textinput.on_change("value", duplicateDistance_textinput_callback)
 
     # ---- maxequal
     def maxequal_textinput_callback(_attr, _old, new):
         config.maxequal = new
 
-    maxequal_textinput = TextInput(title="Max Equal:")
+    maxequal_textinput = TextInput(title="Max Equal:", width=145)
     maxequal_textinput.on_change("value", maxequal_textinput_callback)
 
     # ---- window
     def aps_window_textinput_callback(_attr, _old, new):
         config.aps_window = dict(zip(("x", "y", "z"), re.findall(r"\b\d+\b", new)))
 
-    aps_window_textinput = TextInput(title="Window (x, y, z):")
+    aps_window_textinput = TextInput(title="Window (x, y, z):", width=145)
     aps_window_textinput.on_change("value", aps_window_textinput_callback)
 
     # Adaptive Dynamic Mask Integration (adaptivedynamic)
@@ -264,56 +252,56 @@ def create():
     def adm_window_textinput_callback(_attr, _old, new):
         config.adm_window = dict(zip(("x", "y", "z"), re.findall(r"\b\d+\b", new)))
 
-    adm_window_textinput = TextInput(title="Window (x, y, z):")
+    adm_window_textinput = TextInput(title="Window (x, y, z):", width=145)
     adm_window_textinput.on_change("value", adm_window_textinput_callback)
 
     # ---- border
     def border_textinput_callback(_attr, _old, new):
         config.border = dict(zip(("x", "y", "z"), re.findall(r"\b\d+\b", new)))
 
-    border_textinput = TextInput(title="Border (x, y, z):")
+    border_textinput = TextInput(title="Border (x, y, z):", width=145)
     border_textinput.on_change("value", border_textinput_callback)
 
     # ---- minWindow
     def minWindow_textinput_callback(_attr, _old, new):
         config.minWindow = dict(zip(("x", "y", "z"), re.findall(r"\b\d+\b", new)))
 
-    minWindow_textinput = TextInput(title="Min Window (x, y, z):")
+    minWindow_textinput = TextInput(title="Min Window (x, y, z):", width=145)
     minWindow_textinput.on_change("value", minWindow_textinput_callback)
 
     # ---- reflectionFile
     def reflectionFile_textinput_callback(_attr, _old, new):
         config.reflectionFile = new
 
-    reflectionFile_textinput = TextInput(title="Reflection File:")
+    reflectionFile_textinput = TextInput(title="Reflection File:", width=145)
     reflectionFile_textinput.on_change("value", reflectionFile_textinput_callback)
 
     # ---- targetMonitor
     def targetMonitor_textinput_callback(_attr, _old, new):
         config.targetMonitor = new
 
-    targetMonitor_textinput = TextInput(title="Target Monitor:")
+    targetMonitor_textinput = TextInput(title="Target Monitor:", width=145)
     targetMonitor_textinput.on_change("value", targetMonitor_textinput_callback)
 
     # ---- smoothSize
     def smoothSize_textinput_callback(_attr, _old, new):
         config.smoothSize = new
 
-    smoothSize_textinput = TextInput(title="Smooth Size:")
+    smoothSize_textinput = TextInput(title="Smooth Size:", width=145)
     smoothSize_textinput.on_change("value", smoothSize_textinput_callback)
 
     # ---- loop
     def loop_textinput_callback(_attr, _old, new):
         config.loop = new
 
-    loop_textinput = TextInput(title="Loop:")
+    loop_textinput = TextInput(title="Loop:", width=145)
     loop_textinput.on_change("value", loop_textinput_callback)
 
     # ---- minPeakCount
     def minPeakCount_textinput_callback(_attr, _old, new):
         config.minPeakCount = new
 
-    minPeakCount_textinput = TextInput(title="Min Peak Count:")
+    minPeakCount_textinput = TextInput(title="Min Peak Count:", width=145)
     minPeakCount_textinput.on_change("value", minPeakCount_textinput_callback)
 
     # ---- displacementCurve
@@ -324,95 +312,85 @@ def create():
         config.displacementCurve = maps
 
     displacementCurve_textinput = TextAreaInput(
-        title="Displacement Curve (twotheta, x, y):", height=100
+        title="Displ. Curve (2θ, x, y):", width=145, height=100
     )
     displacementCurve_textinput.on_change("value", displacementCurve_textinput_callback)
 
-    def mode_radio_button_group_callback(active):
-        if active == 0:
+    def algorithm_tabs_callback(_attr, _old, new):
+        if new == 0:
             config.algorithm = "adaptivemaxcog"
-            set_active_widgets("adaptivemaxcog")
         else:
             config.algorithm = "adaptivedynamic"
-            set_active_widgets("adaptivedynamic")
 
-    mode_radio_button_group = RadioButtonGroup(
-        labels=["Adaptive Peak Detection", "Adaptive Dynamic Integration"], active=0
+    algorithm_params = Tabs(
+        tabs=[
+            Panel(
+                child=column(
+                    row(threshold_textinput, shell_textinput, steepness_textinput),
+                    row(duplicateDistance_textinput, maxequal_textinput, aps_window_textinput),
+                ),
+                title="Peak Search",
+            ),
+            Panel(
+                child=column(
+                    row(adm_window_textinput, border_textinput, minWindow_textinput),
+                    row(reflectionFile_textinput, targetMonitor_textinput, smoothSize_textinput),
+                    row(loop_textinput, minPeakCount_textinput, displacementCurve_textinput),
+                ),
+                title="Dynamic Integration",
+            ),
+        ]
     )
-    mode_radio_button_group.on_click(mode_radio_button_group_callback)
-    set_active_widgets("adaptivemaxcog")
+    algorithm_params.on_change("active", algorithm_tabs_callback)
 
     def process_button_callback():
         with tempfile.TemporaryDirectory() as temp_dir:
-            temp_file = temp_dir + "/temp.xml"
+            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(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")
     process_button.on_click(process_button_callback)
 
-    output_log = TextAreaInput(title="Logfile output:", height=600, disabled=True)
-    output_config = TextAreaInput(title="Current config:", height=600, width=400, disabled=True)
+    output_log = TextAreaInput(title="Logfile output:", height=320, width=465, disabled=True)
+    output_res = TextAreaInput(title="Result output:", height=320, width=465, disabled=True)
+    output_config = TextAreaInput(title="Current config:", height=320, width=465, disabled=True)
 
     general_params_layout = column(
-        row(logfile_textinput, logfile_verbosity_select),
+        row(column(Spacer(height=2), upload_div), upload_button),
+        row(logfile_textinput, logfile_verbosity),
         row(filelist_type, filelist_format_textinput),
         filelist_datapath_textinput,
         filelist_ranges_textareainput,
-        crystal_sample_textinput,
-        row(lambda_textinput, zeroOM_textinput),
-        row(zeroSTT_textinput, zeroCHI_textinput),
+        row(crystal_sample_textinput, lambda_textinput),
         ub_textareainput,
-        row(dataFactory_implementation_select, dataFactory_dist1_textinput),
-        reflectionPrinter_format_select,
+        row(zeroOM_textinput, zeroSTT_textinput, zeroCHI_textinput),
+        row(
+            dataFactory_implementation_select,
+            dataFactory_dist1_textinput,
+            dataFactory_dist2_textinput,
+            dataFactory_dist3_textinput,
+        ),
+        row(reflectionPrinter_format_select),
     )
 
-    algorithm_params_layout = column(
-        mode_radio_button_group,
-        row(
-            column(
-                threshold_textinput,
-                shell_textinput,
-                steepness_textinput,
-                duplicateDistance_textinput,
-                maxequal_textinput,
-                aps_window_textinput,
-            ),
-            column(
-                adm_window_textinput,
-                border_textinput,
-                minWindow_textinput,
-                reflectionFile_textinput,
-                targetMonitor_textinput,
-                smoothSize_textinput,
-                loop_textinput,
-                minPeakCount_textinput,
-                displacementCurve_textinput,
-            ),
-        ),
-    )
-
-    tab_layout = column(
-        row(column(Spacer(height=2), upload_div), upload_button),
-        row(
-            general_params_layout,
-            algorithm_params_layout,
-            column(row(output_config, output_log), row(process_button)),
-        ),
+    tab_layout = row(
+        general_params_layout,
+        column(output_config, algorithm_params, row(process_button)),
+        column(output_log, output_res),
     )
 
     async def update_config():
-        with tempfile.TemporaryDirectory() as temp_dir:
-            temp_file = temp_dir + "/debug.xml"
-            config.save_as(temp_file)
-            with open(temp_file) as f_config:
-                output_config.value = f_config.read()
+        output_config.value = config.tostring()
 
     doc.add_periodic_callback(update_config, 1000)
 

pyzebra/app/panel_hdf_viewer.py

@@ -9,11 +9,15 @@ from bokeh.models import (
     BoxEditTool,
     BoxZoomTool,
     Button,
+    CheckboxGroup,
     ColumnDataSource,
     DataRange1d,
+    DataTable,
     Div,
     FileInput,
     Grid,
+    MultiSelect,
+    NumberFormatter,
     HoverTool,
     Image,
     Line,
@@ -22,17 +26,17 @@ from bokeh.models import (
     Panel,
     PanTool,
     Plot,
-    RadioButtonGroup,
     Range1d,
     Rect,
     ResetTool,
     Select,
+    Slider,
     Spacer,
     Spinner,
+    TableColumn,
     TextAreaInput,
     TextInput,
     Title,
-    Toggle,
     WheelZoomTool,
 )
 from bokeh.palettes import Cividis256, Greys256, Plasma256  # pylint: disable=E0611
@@ -41,10 +45,8 @@ import pyzebra
 
 IMAGE_W = 256
 IMAGE_H = 128
-IMAGE_PLOT_W = int(IMAGE_W * 2.5)
-IMAGE_PLOT_H = int(IMAGE_H * 2.5)
-
-PROPOSAL_PATH = "/afs/psi.ch/project/sinqdata/2020/zebra/"
+IMAGE_PLOT_W = int(IMAGE_W * 2) + 52
+IMAGE_PLOT_H = int(IMAGE_H * 2) + 27
 
 
 def create():
@@ -52,26 +54,26 @@ def create():
     roi_selection = {}
 
     def proposal_textinput_callback(_attr, _old, new):
-        full_proposal_path = os.path.join(PROPOSAL_PATH, new.strip())
+        proposal = new.strip()
+        year = new[:4]
+        proposal_path = f"/afs/psi.ch/project/sinqdata/{year}/zebra/{proposal}"
         file_list = []
-        for file in os.listdir(full_proposal_path):
+        for file in os.listdir(proposal_path):
             if file.endswith(".hdf"):
-                file_list.append((os.path.join(full_proposal_path, file), file))
-        filelist.options = file_list
-        filelist.value = file_list[0][0]
+                file_list.append((os.path.join(proposal_path, file), file))
+        file_select.options = file_list
 
-    proposal_textinput = TextInput(title="Enter proposal number:", default_size=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]
-            filelist.value = file_list[0]
+            file_select.options = [(entry, os.path.basename(entry)) for entry in file_list]
 
     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):
@@ -91,7 +93,7 @@ def create():
         )
         image_source.data.update(image=[current_image])
 
-        if auto_toggle.active:
+        if main_auto_checkbox.active:
             im_min = np.min(current_image)
             im_max = np.max(current_image)
 
@@ -102,14 +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]
@@ -121,10 +123,10 @@ def create():
         overview_x = np.mean(h5_data, axis=1)
         overview_y = np.mean(h5_data, axis=2)
 
-        overview_plot_x_image_source.data.update(image=[overview_x], dw=[n_x])
-        overview_plot_y_image_source.data.update(image=[overview_y], dw=[n_y])
+        overview_plot_x_image_source.data.update(image=[overview_x], dw=[n_x], dh=[n_im])
+        overview_plot_y_image_source.data.update(image=[overview_y], dw=[n_y], dh=[n_im])
 
-        if proj_auto_toggle.active:
+        if proj_auto_checkbox.active:
             im_min = min(np.min(overview_x), np.min(overview_y))
             im_max = max(np.max(overview_x), np.max(overview_y))
 
@@ -136,48 +138,69 @@ def create():
             overview_plot_x_image_glyph.color_mapper.high = im_max
             overview_plot_y_image_glyph.color_mapper.high = im_max
 
-        if frame_button_group.active == 0:  # Frame
-            overview_plot_x.axis[1].axis_label = "Frame"
-            overview_plot_y.axis[1].axis_label = "Frame"
+        frame_range.start = 0
+        frame_range.end = n_im
+        frame_range.reset_start = 0
+        frame_range.reset_end = n_im
+        frame_range.bounds = (0, n_im)
 
-            overview_plot_x_image_source.data.update(y=[0], dh=[n_im])
-            overview_plot_y_image_source.data.update(y=[0], dh=[n_im])
+        scan_motor = det_data["scan_motor"]
+        overview_plot_y.axis[1].axis_label = f"Scanning motor, {scan_motor}"
 
-        elif frame_button_group.active == 1:  # Variable angle
-            scan_motor = det_data["scan_motor"]
-            overview_plot_x.axis[1].axis_label = scan_motor
-            overview_plot_y.axis[1].axis_label = scan_motor
+        var = det_data[scan_motor]
+        var_start = var[0]
+        var_end = var[-1] + (var[-1] - var[0]) / (n_im - 1)
 
-            var = det_data[scan_motor]
-            var_start = var[0]
-            var_end = (var[-1] - var[0]) * n_im / (n_im - 1)
-            overview_plot_x_image_source.data.update(y=[var_start], dh=[var_end])
-            overview_plot_y_image_source.data.update(y=[var_start], dh=[var_end])
+        scanning_motor_range.start = var_start
+        scanning_motor_range.end = var_end
+        scanning_motor_range.reset_start = var_start
+        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:")
-    filelist.on_change("value", filelist_callback)
+    file_select = MultiSelect(title="Available .hdf files:", width=210, height=250)
+    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)
-    index_spinner.on_change("value", index_spinner_callback)
+    index_slider = Slider(value=0, start=0, end=1, show_value=False, width=400)
+
+    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)),
@@ -310,15 +333,18 @@ def create():
     )
     plot.toolbar.active_scroll = wheelzoomtool
 
-    # shared frame range
-    frame_range = DataRange1d()
+    # shared frame ranges
+    frame_range = Range1d(0, 1, bounds=(0, 1))
+    scanning_motor_range = Range1d(0, 1, bounds=(0, 1))
+
     det_x_range = Range1d(0, IMAGE_W, bounds=(0, IMAGE_W))
     overview_plot_x = Plot(
         title=Title(text="Projections on X-axis"),
         x_range=det_x_range,
         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
@@ -354,8 +380,9 @@ def create():
         title=Title(text="Projections on Y-axis"),
         x_range=det_y_range,
         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
@@ -369,7 +396,12 @@ def create():
     # ---- axes
     overview_plot_y.add_layout(LinearAxis(axis_label="Coordinate Y, pix"), place="below")
     overview_plot_y.add_layout(
-        LinearAxis(axis_label="Frame", major_label_orientation="vertical"), place="left"
+        LinearAxis(
+            y_range_name="scanning_motor",
+            axis_label="Scanning motor",
+            major_label_orientation="vertical",
+        ),
+        place="right",
     )
 
     # ---- grid lines
@@ -386,16 +418,10 @@ def create():
         overview_plot_y_image_source, overview_plot_y_image_glyph, name="image_glyph"
     )
 
-    def frame_button_group_callback(_active):
-        update_overview_plot()
-
-    frame_button_group = RadioButtonGroup(labels=["Frames", "Variable Angle"], active=0)
-    frame_button_group.on_click(frame_button_group_callback)
-
     roi_avg_plot = Plot(
         x_range=DataRange1d(),
         y_range=DataRange1d(),
-        plot_height=200,
+        plot_height=150,
         plot_width=IMAGE_PLOT_W,
         toolbar_location="left",
     )
@@ -426,13 +452,13 @@ def create():
         overview_plot_x_image_glyph.color_mapper = LinearColorMapper(palette=cmap_dict[new])
         overview_plot_y_image_glyph.color_mapper = LinearColorMapper(palette=cmap_dict[new])
 
-    colormap = Select(title="Colormap:", options=list(cmap_dict.keys()), default_size=145)
+    colormap = Select(title="Colormap:", options=list(cmap_dict.keys()), width=210)
     colormap.on_change("value", colormap_callback)
     colormap.value = "plasma"
 
     STEP = 1
-    # ---- colormap auto toggle button
-    def auto_toggle_callback(state):
+
+    def main_auto_checkbox_callback(state):
         if state:
             display_min_spinner.disabled = True
             display_max_spinner.disabled = True
@@ -442,45 +468,43 @@ def create():
 
         update_image()
 
-    auto_toggle = Toggle(
-        label="Main Auto Range", active=True, button_type="default", default_size=125
+    main_auto_checkbox = CheckboxGroup(
+        labels=["Main Auto Range"], active=[0], width=145, margin=[10, 5, 0, 5]
     )
-    auto_toggle.on_click(auto_toggle_callback)
+    main_auto_checkbox.on_click(main_auto_checkbox_callback)
 
-    # ---- colormap display max value
     def display_max_spinner_callback(_attr, _old_value, new_value):
         display_min_spinner.high = new_value - STEP
         image_glyph.color_mapper.high = new_value
 
     display_max_spinner = Spinner(
-        title="Max Value:",
         low=0 + STEP,
         value=1,
         step=STEP,
-        disabled=auto_toggle.active,
-        default_size=80,
+        disabled=bool(main_auto_checkbox.active),
+        width=100,
+        height=31,
     )
     display_max_spinner.on_change("value", display_max_spinner_callback)
 
-    # ---- colormap display min value
     def display_min_spinner_callback(_attr, _old_value, new_value):
         display_max_spinner.low = new_value + STEP
         image_glyph.color_mapper.low = new_value
 
     display_min_spinner = Spinner(
-        title="Min Value:",
         low=0,
         high=1 - STEP,
         value=0,
         step=STEP,
-        disabled=auto_toggle.active,
-        default_size=80,
+        disabled=bool(main_auto_checkbox.active),
+        width=100,
+        height=31,
     )
     display_min_spinner.on_change("value", display_min_spinner_callback)
 
     PROJ_STEP = 0.1
-    # ---- proj colormap auto toggle button
-    def proj_auto_toggle_callback(state):
+
+    def proj_auto_checkbox_callback(state):
         if state:
             proj_display_min_spinner.disabled = True
             proj_display_max_spinner.disabled = True
@@ -490,41 +514,39 @@ def create():
 
         update_overview_plot()
 
-    proj_auto_toggle = Toggle(
-        label="Proj Auto Range", active=True, button_type="default", default_size=125
+    proj_auto_checkbox = CheckboxGroup(
+        labels=["Projections Auto Range"], active=[0], width=145, margin=[10, 5, 0, 5]
     )
-    proj_auto_toggle.on_click(proj_auto_toggle_callback)
+    proj_auto_checkbox.on_click(proj_auto_checkbox_callback)
 
-    # ---- proj colormap display max value
     def proj_display_max_spinner_callback(_attr, _old_value, new_value):
         proj_display_min_spinner.high = new_value - PROJ_STEP
         overview_plot_x_image_glyph.color_mapper.high = new_value
         overview_plot_y_image_glyph.color_mapper.high = new_value
 
     proj_display_max_spinner = Spinner(
-        title="Max Value:",
         low=0 + PROJ_STEP,
         value=1,
         step=PROJ_STEP,
-        disabled=proj_auto_toggle.active,
-        default_size=80,
+        disabled=bool(proj_auto_checkbox.active),
+        width=100,
+        height=31,
     )
     proj_display_max_spinner.on_change("value", proj_display_max_spinner_callback)
 
-    # ---- proj colormap display min value
     def proj_display_min_spinner_callback(_attr, _old_value, new_value):
         proj_display_max_spinner.low = new_value + PROJ_STEP
         overview_plot_x_image_glyph.color_mapper.low = new_value
         overview_plot_y_image_glyph.color_mapper.low = new_value
 
     proj_display_min_spinner = Spinner(
-        title="Min Value:",
         low=0,
         high=1 - PROJ_STEP,
         value=0,
         step=PROJ_STEP,
-        disabled=proj_auto_toggle.active,
-        default_size=80,
+        disabled=bool(proj_auto_checkbox.active),
+        width=100,
+        height=31,
     )
     proj_display_min_spinner.on_change("value", proj_display_min_spinner_callback)
 
@@ -533,7 +555,7 @@ def create():
         h, k, l = calculate_hkl(det_data, index)
         image_source.data.update(h=[h], k=[k], l=[l])
 
-    hkl_button = Button(label="Calculate hkl (slow)")
+    hkl_button = Button(label="Calculate hkl (slow)", width=210)
     hkl_button.on_click(hkl_button_callback)
 
     selection_list = TextAreaInput(rows=7)
@@ -549,7 +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:
@@ -560,32 +582,38 @@ 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=145, disabled=True
+    metadata_table_source = ColumnDataSource(dict(geom=[""], temp=[None], mf=[None]))
+    num_formatter = NumberFormatter(format="0.00", nan_format="")
+    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,
     )
-    temp_spinner = Spinner(title="Temperature:", format="0.00", width=145, disabled=True)
-    geometry_textinput = TextInput(title="Geometry:", disabled=True)
 
     # 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(
-        row(colormap),
-        row(column(Spacer(height=19), auto_toggle), display_max_spinner, display_min_spinner),
-        row(
-            column(Spacer(height=19), proj_auto_toggle),
-            proj_display_max_spinner,
-            proj_display_min_spinner,
-        ),
+        colormap,
+        main_auto_checkbox,
+        row(display_min_spinner, display_max_spinner),
+        proj_auto_checkbox,
+        row(proj_display_min_spinner, proj_display_max_spinner),
     )
-    hkl_layout = column(geometry_textinput, hkl_button)
-    params_layout = row(mf_spinner, temp_spinner)
 
     layout_controls = row(
         column(selection_button, selection_list),
         Spacer(width=20),
-        column(frame_button_group, colormap_layout),
-        Spacer(width=20),
-        column(index_spinner, params_layout, hkl_layout),
+        column(
+            row(index_spinner, column(Spacer(height=25), index_slider)), metadata_table, hkl_button
+        ),
     )
 
     layout_overview = column(
@@ -598,13 +626,8 @@ def create():
     )
 
     tab_layout = row(
-        column(
-            row(
-                proposal_textinput, filelist, Spacer(width=100), column(upload_div, upload_button),
-            ),
-            layout_overview,
-            layout_controls,
-        ),
+        column(import_layout, colormap_layout),
+        column(layout_overview, layout_controls),
         column(roi_avg_plot, layout_image),
     )
 

pyzebra/app/panel_param_study.py

@@ -11,6 +11,7 @@ from bokeh.models import (
     BasicTicker,
     Button,
     CheckboxEditor,
+    CheckboxGroup,
     ColumnDataSource,
     CustomJS,
     DataRange1d,
@@ -40,7 +41,6 @@ from bokeh.models import (
     Tabs,
     TextAreaInput,
     TextInput,
-    Toggle,
     WheelZoomTool,
     Whisker,
 )
@@ -66,8 +66,6 @@ for (let i = 0; i < js_data.data['fname'].length; i++) {
 }
 """
 
-PROPOSAL_PATH = "/afs/psi.ch/project/sinqdata/2020/zebra/"
-
 
 def color_palette(n_colors):
     palette = itertools.cycle(Category10[10])
@@ -80,14 +78,16 @@ def create():
     js_data = ColumnDataSource(data=dict(content=["", ""], fname=["", ""]))
 
     def proposal_textinput_callback(_attr, _old, new):
-        full_proposal_path = os.path.join(PROPOSAL_PATH, new.strip())
-        dat_file_list = []
-        for file in os.listdir(full_proposal_path):
-            if file.endswith(".dat"):
-                dat_file_list.append((os.path.join(full_proposal_path, file), file))
-        file_select.options = dat_file_list
+        proposal = new.strip()
+        year = new[:4]
+        proposal_path = f"/afs/psi.ch/project/sinqdata/{year}/zebra/{proposal}"
+        file_list = []
+        for file in os.listdir(proposal_path):
+            if file.endswith((".ccl", ".dat")):
+                file_list.append((os.path.join(proposal_path, file), file))
+        file_select.options = file_list
 
-    proposal_textinput = TextInput(title="Proposal number:", default_size=200)
+    proposal_textinput = TextInput(title="Proposal number:", width=210)
     proposal_textinput.on_change("value", proposal_textinput_callback)
 
     def _init_datatable():
@@ -108,11 +108,7 @@ def create():
 
         param_select.value = "user defined"
 
-    def file_select_callback(_attr, _old, _new):
-        pass
-
-    file_select = MultiSelect(title="Available .dat files:", default_size=200, height=250)
-    file_select.on_change("value", file_select_callback)
+    file_select = MultiSelect(title="Available .ccl/.dat files:", width=210, height=250)
 
     def file_open_button_callback():
         nonlocal det_data
@@ -131,7 +127,7 @@ def create():
 
         _init_datatable()
 
-    file_open_button = Button(label="Open New", default_size=100)
+    file_open_button = Button(label="Open New", width=100)
     file_open_button.on_click(file_open_button_callback)
 
     def file_append_button_callback():
@@ -145,7 +141,7 @@ def create():
 
         _init_datatable()
 
-    file_append_button = Button(label="Append", default_size=100)
+    file_append_button = Button(label="Append", width=100)
     file_append_button.on_click(file_append_button_callback)
 
     def upload_button_callback(_attr, _old, new):
@@ -165,8 +161,8 @@ def create():
 
         _init_datatable()
 
-    upload_div = Div(text="or upload new .dat files:", margin=(5, 5, 0, 5))
-    upload_button = FileInput(accept=".dat", multiple=True, default_size=200)
+    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)
     upload_button.on_change("value", upload_button_callback)
 
     def append_upload_button_callback(_attr, _old, new):
@@ -181,7 +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, default_size=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):
@@ -297,7 +293,7 @@ def create():
         plot_bkg_source, Line(x="x", y="y", line_color="green", line_dash="dashed")
     )
 
-    plot_peak_source = ColumnDataSource(dict(xs=[0], ys=[0]))
+    plot_peak_source = ColumnDataSource(dict(xs=[[0]], ys=[[0]]))
     plot_peak = plot.add_glyph(
         plot_peak_source, MultiLine(xs="xs", ys="ys", line_color="red", line_dash="dashed")
     )
@@ -390,7 +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=[
@@ -427,20 +428,20 @@ def create():
         title="Parameter:",
         options=["user defined", "temp", "mf", "h", "k", "l"],
         value="user defined",
-        default_size=145,
+        width=145,
     )
     param_select.on_change("value", param_select_callback)
 
     def fit_from_spinner_callback(_attr, _old, new):
         fit_from_span.location = new
 
-    fit_from_spinner = Spinner(title="Fit from:", default_size=145)
+    fit_from_spinner = Spinner(title="Fit from:", width=145)
     fit_from_spinner.on_change("value", fit_from_spinner_callback)
 
     def fit_to_spinner_callback(_attr, _old, new):
         fit_to_span.location = new
 
-    fit_to_spinner = Spinner(title="to:", default_size=145)
+    fit_to_spinner = Spinner(title="to:", width=145)
     fit_to_spinner.on_change("value", fit_to_spinner_callback)
 
     def fitparams_add_dropdown_callback(click):
@@ -459,7 +460,7 @@ def create():
             ("Pseudo Voigt", "pvoigt"),
             # ("Pseudo Voigt1", "pseudovoigt1"),
         ],
-        default_size=145,
+        width=145,
     )
     fitparams_add_dropdown.on_click(fitparams_add_dropdown_callback)
 
@@ -479,7 +480,7 @@ def create():
         else:
             fitparams_table_source.data.update(dict(param=[], value=[], vary=[], min=[], max=[]))
 
-    fitparams_select = MultiSelect(options=[], height=120, default_size=145)
+    fitparams_select = MultiSelect(options=[], height=120, width=145)
     fitparams_select.tags = [0]
     fitparams_select.on_change("value", fitparams_select_callback)
 
@@ -494,7 +495,7 @@ def create():
 
             fitparams_select.value = []
 
-    fitparams_remove_button = Button(label="Remove fit function", default_size=145)
+    fitparams_remove_button = Button(label="Remove fit function", width=145)
     fitparams_remove_button.on_click(fitparams_remove_button_callback)
 
     def fitparams_factory(function):
@@ -516,6 +517,14 @@ def create():
             param=params, value=[None] * n, vary=[True] * n, min=[None] * n, max=[None] * n,
         )
 
+        if function == "linear":
+            fitparams["value"] = [0, 1]
+            fitparams["vary"] = [False, True]
+            fitparams["min"] = [None, 0]
+
+        elif function == "gaussian":
+            fitparams["min"] = [0, None, None]
+
         return fitparams
 
     fitparams_table_source = ColumnDataSource(dict(param=[], value=[], vary=[], min=[], max=[]))
@@ -552,7 +561,7 @@ def create():
         _update_plot()
         _update_table()
 
-    fit_all_button = Button(label="Fit All", button_type="primary", default_size=145)
+    fit_all_button = Button(label="Fit All", button_type="primary", width=145)
     fit_all_button.on_click(fit_all_button_callback)
 
     def fit_button_callback():
@@ -564,22 +573,26 @@ def create():
         _update_plot()
         _update_table()
 
-    fit_button = Button(label="Fit Current", default_size=145)
+    fit_button = Button(label="Fit Current", width=145)
     fit_button.on_click(fit_button_callback)
 
+    def area_method_radiobutton_callback(_handler):
+        _update_preview()
+
     area_method_radiobutton = RadioButtonGroup(
-        labels=["Fit area", "Int area"], active=0, default_size=145, disabled=True
+        labels=["Fit area", "Int area"], active=0, width=145, disabled=True
     )
+    area_method_radiobutton.on_click(area_method_radiobutton_callback)
 
-    bin_size_spinner = Spinner(
-        title="Bin size:", value=1, low=1, step=1, default_size=145, disabled=True
-    )
+    def lorentz_checkbox_callback(_handler):
+        _update_preview()
 
-    lorentz_toggle = Toggle(label="Lorentz Correction", default_size=145)
+    lorentz_checkbox = CheckboxGroup(labels=["Lorentz Correction"], width=145, margin=[13, 5, 5, 5])
+    lorentz_checkbox.on_click(lorentz_checkbox_callback)
 
-    export_preview_textinput = TextAreaInput(title="Export preview:", width=450, height=400)
+    export_preview_textinput = TextAreaInput(title="Export file preview:", width=450, height=400)
 
-    def preview_button_callback():
+    def _update_preview():
         with tempfile.TemporaryDirectory() as temp_dir:
             temp_file = temp_dir + "/temp"
             export_data = []
@@ -591,7 +604,7 @@ def create():
                 export_data,
                 temp_file,
                 area_method=AREA_METHODS[int(area_method_radiobutton.active)],
-                lorentz=lorentz_toggle.active,
+                lorentz=bool(lorentz_checkbox.active),
             )
 
             exported_content = ""
@@ -609,10 +622,7 @@ def create():
             js_data.data.update(content=file_content)
             export_preview_textinput.value = exported_content
 
-    preview_button = Button(label="Preview", default_size=220)
-    preview_button.on_click(preview_button_callback)
-
-    save_button = Button(label="Download preview", button_type="success", default_size=220)
+    save_button = Button(label="Download File", button_type="success", width=220)
     save_button.js_on_click(CustomJS(args={"js_data": js_data}, code=javaScript))
 
     fitpeak_controls = row(
@@ -621,8 +631,7 @@ def create():
         Spacer(width=20),
         column(
             row(fit_from_spinner, fit_to_spinner),
-            row(bin_size_spinner, column(Spacer(height=19), lorentz_toggle)),
-            row(area_method_radiobutton),
+            row(area_method_radiobutton, lorentz_checkbox),
             row(fit_button, fit_all_button),
         ),
     )
@@ -639,7 +648,7 @@ def create():
         append_upload_button,
     )
 
-    export_layout = column(export_preview_textinput, row(preview_button, save_button))
+    export_layout = column(export_preview_textinput, row(save_button))
 
     tab_layout = column(
         row(import_layout, scan_layout, plots, Spacer(width=30), export_layout),

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
@@ -28,15 +27,19 @@ def create():
     lattice_const_textinput = TextInput(
         title="Lattice constants:", value="8.3211,8.3211,8.3211,90.00,90.00,90.00"
     )
-    max_res_spinner = Spinner(title="max-res", value=2, step=0.01)
-    seed_pool_size_spinner = Spinner(title="seed-pool-size", value=5, step=0.01)
-    seed_len_tol_spinner = Spinner(title="seed-len-tol", value=0.02, step=0.01)
-    seed_angle_tol_spinner = Spinner(title="seed-angle-tol", value=1, step=0.01)
-    eval_hkl_tol_spinner = Spinner(title="eval-hkl-tol", value=0.15, step=0.01)
+    max_res_spinner = Spinner(title="max-res:", value=2, step=0.01, width=145)
+    seed_pool_size_spinner = Spinner(title="seed-pool-size:", value=5, step=0.01, width=145)
+    seed_len_tol_spinner = Spinner(title="seed-len-tol:", value=0.02, step=0.01, width=145)
+    seed_angle_tol_spinner = Spinner(title="seed-angle-tol:", value=1, step=0.01, width=145)
+    eval_hkl_tol_spinner = Spinner(title="eval-hkl-tol:", value=0.15, step=0.01, width=145)
 
     diff_vec = []
+    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")
@@ -51,7 +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),
@@ -68,13 +71,17 @@ def create():
 
             diff_vec = prepare_event_file(temp_event_file, roi_dict, path_prefix_textinput.value)
 
+            print(f"Content of {temp_event_file}:")
+            with open(temp_event_file) as f:
+                print(f.read())
+
             comp_proc = subprocess.run(
                 [
                     "mpiexec",
                     "-n",
                     "2",
                     "python",
-                    "spind/SPIND.py",
+                    os.path.expanduser("~/spind/SPIND.py"),
                     temp_peak_list_dir,
                     temp_hkl_file,
                     "-o",
@@ -96,9 +103,12 @@ def create():
             print(" ".join(comp_proc.args))
             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(os.path.join(temp_dir, "spind.txt")) as f_out:
-                    spind_res = defaultdict(list)
+                with open(spind_out_file) as f_out:
                     for line in f_out:
                         c1, c2, c3, c4, c5, *c_rest = line.split()
                         spind_res["label"].append(c1)
@@ -109,32 +119,42 @@ 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 = np.linalg.inv(np.transpose(ub_matrix_spind)) * 1e10
-                        spind_res["ub_matrix"].append(ub_matrix)
+                        ub_matrix_spind = np.transpose(np.array(vals).reshape(3, 3))
+                        ub_matrix = np.linalg.inv(ub_matrix_spind)
+                        ub_matrices.append(ub_matrix)
+                        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:
+                    print(f.read())
 
             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)
 
-    hkl_textareainput = TextAreaInput(title="hkl values:", rows=7)
+    ub_matrix_textareainput = TextAreaInput(title="UB matrix:", rows=7, width=400)
+    hkl_textareainput = TextAreaInput(title="hkl values:", rows=7, width=400)
 
     def results_table_select_callback(_attr, old, new):
         if new:
             ind = new[0]
-            ub_matrix = results_table_source.data["ub_matrix"][ind]
+            ub_matrix = ub_matrices[ind]
             res = ""
             for vec in diff_vec:
-                res += f"{vec @ ub_matrix}\n"
+                res += f"{ub_matrix @ vec}\n"
+            ub_matrix_textareainput.value = str(ub_matrix * 1e10)
             hkl_textareainput.value = res
         else:
-            hkl_textareainput.value = None
+            ub_matrix_textareainput.value = ""
+            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=[
@@ -143,10 +163,10 @@ def create():
             TableColumn(field="match_rate", title="Match Rate", width=100),
             TableColumn(field="matched_peaks", title="Matched Peaks", width=100),
             TableColumn(field="column_5", title="", width=100),
-            TableColumn(field="ub_matrix", title="UB Matrix", width=250),
+            TableColumn(field="ub_matrix", title="UB Matrix", width=700),
         ],
         height=300,
-        width=700,
+        width=1200,
         autosize_mode="none",
         index_position=None,
     )
@@ -158,14 +178,12 @@ def create():
             path_prefix_textinput,
             selection_list,
             lattice_const_textinput,
-            max_res_spinner,
-            seed_pool_size_spinner,
-            seed_len_tol_spinner,
-            seed_angle_tol_spinner,
-            eval_hkl_tol_spinner,
+            row(max_res_spinner, seed_pool_size_spinner),
+            row(seed_len_tol_spinner, seed_angle_tol_spinner),
+            row(eval_hkl_tol_spinner),
             process_button,
         ),
-        column(results_table, row(hkl_textareainput)),
+        column(results_table, row(ub_matrix_textareainput, hkl_textareainput)),
     )
 
     return Panel(child=tab_layout, title="spind")
@@ -244,9 +262,10 @@ def prepare_event_file(export_filename, roi_dict, path_prefix=""):
                 ga, nu = pyzebra.det2pol(ddist, gamma, nu, x_pos, y_pos)
                 diff_vector = pyzebra.z1frmd(wave, ga, omega, chi, phi, nu)
                 d_spacing = float(pyzebra.dandth(wave, diff_vector)[0])
-                dv1, dv2, dv3 = diff_vector.flatten() * 1e10
+                diff_vector = diff_vector.flatten() * 1e10
+                dv1, dv2, dv3 = diff_vector
 
-                diff_vec.append(diff_vector.flatten())
+                diff_vec.append(diff_vector)
 
                 f.write(f"{x_pos} {y_pos} {intensity} {snr_cnts} {dv1} {dv2} {dv3} {d_spacing}\n")
 

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:
-                area_n = param.value
-                area_s = param.stderr
+                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
-            area_s = 0
-
-        if area_n is None or area_s is None:
-            print(f"Couldn't export scan: {scan['idx']}")
-            continue
+            # no peak functions in a fit model
+            area_n = np.nan
+            area_s = np.nan
 
         # 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: