Updating for version 0.1.2

* allow user to specify anatric path

pyzebra/__init__.py

@@ -1,10 +1,9 @@
-import pyzebra.ccl_dict_operation
 from pyzebra.anatric import *
 from pyzebra.ccl_findpeaks import ccl_findpeaks
-from pyzebra.comm_export import export_comm
 from pyzebra.fit2 import fitccl
 from pyzebra.h5 import *
-from pyzebra.load_1D import load_1D, parse_1D
+from pyzebra.ccl_io import load_1D, parse_1D, export_comm
+from pyzebra.param_study_moduls import add_dict, auto, merge, scan_dict
 from pyzebra.xtal import *
 
-__version__ = "0.1.0"
+__version__ = "0.1.2"

pyzebra/anatric.py

@@ -2,7 +2,6 @@ import subprocess
 import xml.etree.ElementTree as ET
 
 
-ANATRIC_PATH = "/afs/psi.ch/project/sinq/rhel7/bin/anatric"
 DATA_FACTORY_IMPLEMENTATION = [
     "trics",
     "morph",
@@ -24,8 +23,8 @@ REFLECTION_PRINTER_FORMATS = [
 ALGORITHMS = ["adaptivemaxcog", "adaptivedynamic"]
 
 
-def anatric(config_file):
+def anatric(config_file, anatric_path="/afs/psi.ch/project/sinq/rhel7/bin/anatric"):
-    subprocess.run([ANATRIC_PATH, config_file], check=True)
+    subprocess.run([anatric_path, config_file], check=True)
 
 
 class AnatricConfig:

pyzebra/app/app.py

@@ -1,4 +1,3 @@
-import argparse
 import logging
 import sys
 from io import StringIO
@@ -11,14 +10,8 @@ import panel_ccl_integrate
 import panel_hdf_anatric
 import panel_hdf_viewer
 
-parser = argparse.ArgumentParser(
-    prog="pyzebra", formatter_class=argparse.ArgumentDefaultsHelpFormatter
-)
-
-args = parser.parse_args()
 
 doc = curdoc()
-doc.title = "pyzebra"
 
 sys.stdout = StringIO()
 stdout_textareainput = TextAreaInput(title="print output:", height=150)
@@ -26,7 +19,7 @@ stdout_textareainput = TextAreaInput(title="print output:", height=150)
 bokeh_stream = StringIO()
 bokeh_handler = logging.StreamHandler(bokeh_stream)
 bokeh_handler.setFormatter(logging.Formatter(logging.BASIC_FORMAT))
-bokeh_logger = logging.getLogger('bokeh')
+bokeh_logger = logging.getLogger("bokeh")
 bokeh_logger.addHandler(bokeh_handler)
 bokeh_log_textareainput = TextAreaInput(title="server output:", height=150)
 

pyzebra/app/handler.py

@@ -0,0 +1,30 @@
+from bokeh.application.handlers import Handler
+
+
+class PyzebraHandler(Handler):
+    """Provides a mechanism for generic bokeh applications to build up new streamvis documents.
+    """
+
+    def __init__(self, anatric_path):
+        """Initialize a pyzebra handler for bokeh applications.
+
+        Args:
+            args (Namespace): Command line parsed arguments.
+        """
+        super().__init__()  # no-op
+
+        self.anatric_path = anatric_path
+
+    def modify_document(self, doc):
+        """Modify an application document with pyzebra specific features.
+
+        Args:
+            doc (Document) : A bokeh Document to update in-place
+
+        Returns:
+            Document
+        """
+        doc.title = "pyzebra"
+        doc.anatric_path = self.anatric_path
+
+        return doc

pyzebra/app/panel_ccl_integrate.py

@@ -2,6 +2,7 @@ import base64
 import io
 import os
 import tempfile
+from copy import deepcopy
 
 import numpy as np
 from bokeh.layouts import column, row
@@ -9,6 +10,7 @@ from bokeh.models import (
     Asterisk,
     BasicTicker,
     Button,
+    CheckboxEditor,
     ColumnDataSource,
     CustomJS,
     DataRange1d,
@@ -19,8 +21,10 @@ from bokeh.models import (
     Line,
     LinearAxis,
     Panel,
+    PanTool,
     Plot,
     RadioButtonGroup,
+    ResetTool,
     Scatter,
     Select,
     Spacer,
@@ -30,6 +34,7 @@ from bokeh.models import (
     TextAreaInput,
     TextInput,
     Toggle,
+    WheelZoomTool,
     Whisker,
 )
 
@@ -60,7 +65,7 @@ def create():
     js_data = ColumnDataSource(data=dict(cont=[], ext=[]))
 
     def proposal_textinput_callback(_attr, _old, new):
-        ccl_path = os.path.join(PROPOSAL_PATH, new)
+        ccl_path = os.path.join(PROPOSAL_PATH, new.strip())
         ccl_file_list = []
         for file in os.listdir(ccl_path):
             if file.endswith(".ccl"):
@@ -71,23 +76,30 @@ def create():
     proposal_textinput = TextInput(title="Enter proposal number:", default_size=145)
     proposal_textinput.on_change("value", proposal_textinput_callback)
 
-    def ccl_file_select_callback(_attr, _old, new):
+    def _init_datatable():
-        nonlocal det_data
-        with open(new) as file:
-            _, ext = os.path.splitext(new)
-            det_data = pyzebra.parse_1D(file, ext)
-
         scan_list = list(det_data["scan"].keys())
         hkl = [
             f'{int(m["h_index"])} {int(m["k_index"])} {int(m["l_index"])}'
             for m in det_data["scan"].values()
         ]
         scan_table_source.data.update(
-            scan=scan_list, hkl=hkl, peaks=[0] * len(scan_list), fit=[0] * len(scan_list)
+            scan=scan_list,
+            hkl=hkl,
+            peaks=[0] * len(scan_list),
+            fit=[0] * len(scan_list),
+            export=[True] * len(scan_list),
         )
         scan_table_source.selected.indices = []
         scan_table_source.selected.indices = [0]
 
+    def ccl_file_select_callback(_attr, _old, new):
+        nonlocal det_data
+        with open(new) as file:
+            _, ext = os.path.splitext(new)
+            det_data = pyzebra.parse_1D(file, ext)
+
+        _init_datatable()
+
     ccl_file_select = Select(title="Available .ccl files")
     ccl_file_select.on_change("value", ccl_file_select_callback)
 
@@ -97,30 +109,35 @@ def create():
             _, ext = os.path.splitext(upload_button.filename)
             det_data = pyzebra.parse_1D(file, ext)
 
-        scan_list = list(det_data["scan"].keys())
+        _init_datatable()
-        hkl = [
-            f'{int(m["h_index"])} {int(m["k_index"])} {int(m["l_index"])}'
-            for m in det_data["scan"].values()
-        ]
-        scan_table_source.data.update(
-            scan=scan_list, hkl=hkl, peaks=[0] * len(scan_list), fit=[0] * len(scan_list)
-        )
-        scan_table_source.selected.indices = []
-        scan_table_source.selected.indices = [0]
 
     upload_button = FileInput(accept=".ccl")
     upload_button.on_change("value", upload_button_callback)
 
+    def append_upload_button_callback(_attr, _old, new):
+        nonlocal det_data
+        with io.StringIO(base64.b64decode(new).decode()) as file:
+            _, ext = os.path.splitext(append_upload_button.filename)
+            append_data = pyzebra.parse_1D(file, ext)
+
+        added = pyzebra.add_dict(det_data, append_data)
+        scan_result = pyzebra.auto(pyzebra.scan_dict(added))
+        det_data = pyzebra.merge(added, added, scan_result)
+
+        _init_datatable()
+
+    append_upload_button = FileInput(accept=".ccl,.dat")
+    append_upload_button.on_change("value", append_upload_button_callback)
+
     def _update_table():
         num_of_peaks = [scan.get("num_of_peaks", 0) for scan in det_data["scan"].values()]
         fit_ok = [(1 if "fit" in scan else 0) for scan in det_data["scan"].values()]
         scan_table_source.data.update(peaks=num_of_peaks, fit=fit_ok)
 
-    def _update_plot(ind):
+    def _update_plot(scan):
         nonlocal peak_pos_textinput_lock
         peak_pos_textinput_lock = True
 
-        scan = det_data["scan"][ind]
         y = scan["Counts"]
         x = scan["om"]
 
@@ -145,18 +162,17 @@ def create():
 
         fit = scan.get("fit")
         if fit is not None:
+            x = scan["fit"]["x_fit"]
             plot_gauss_source.data.update(x=x, y=scan["fit"]["comps"]["gaussian"])
             plot_bkg_source.data.update(x=x, y=scan["fit"]["comps"]["background"])
             params = fit["result"].params
             fit_output_textinput.value = (
-                "%s \n"
                 "Gaussian: centre = %9.4f, sigma = %9.4f, area = %9.4f \n"
                 "background: slope = %9.4f, intercept = %9.4f \n"
                 "Int. area = %9.4f +/- %9.4f \n"
                 "fit area = %9.4f +/- %9.4f \n"
                 "ratio((fit-int)/fit) = %9.4f"
                 % (
-                    ind,
                     params["g_cen"].value,
                     params["g_width"].value,
                     params["g_amp"].value,
@@ -188,13 +204,7 @@ def create():
             numfit_max_span.location = None
 
     # Main plot
-    plot = Plot(
+    plot = Plot(x_range=DataRange1d(), y_range=DataRange1d(), plot_height=400, plot_width=700)
-        x_range=DataRange1d(),
-        y_range=DataRange1d(),
-        plot_height=400,
-        plot_width=700,
-        toolbar_location=None,
-    )
 
     plot.add_layout(LinearAxis(axis_label="Counts"), place="left")
     plot.add_layout(LinearAxis(axis_label="Omega"), place="below")
@@ -226,12 +236,28 @@ def create():
     numfit_max_span = Span(location=None, dimension="height", line_dash="dashed")
     plot.add_layout(numfit_max_span)
 
-    # Scan select
+    plot.add_tools(PanTool(), WheelZoomTool(), ResetTool())
-    def scan_table_callback(_attr, _old, new):
+    plot.toolbar.logo = None
-        if new:
-            _update_plot(scan_table_source.data["scan"][new[-1]])
 
-    scan_table_source = ColumnDataSource(dict(scan=[], hkl=[], peaks=[], fit=[]))
+    # Scan select
+    def scan_table_select_callback(_attr, old, 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
+            scan_table_source.selected.indices = old
+            return
+
+        if len(old) > 1:
+            # skip unnecessary update caused by selection drop
+            return
+
+        _update_plot(det_data["scan"][scan_table_source.data["scan"][new[0]]])
+
+    scan_table_source = ColumnDataSource(dict(scan=[], hkl=[], peaks=[], fit=[], export=[]))
     scan_table = DataTable(
         source=scan_table_source,
         columns=[
@@ -239,25 +265,30 @@ def create():
             TableColumn(field="hkl", title="hkl"),
             TableColumn(field="peaks", title="Peaks"),
             TableColumn(field="fit", title="Fit"),
+            TableColumn(field="export", title="Export", editor=CheckboxEditor()),
         ],
-        width=200,
+        width=250,
         index_position=None,
+        editable=True,
     )
 
-    scan_table_source.selected.on_change("indices", scan_table_callback)
+    scan_table_source.selected.on_change("indices", scan_table_select_callback)
+
+    def _get_selected_scan():
+        selected_index = scan_table_source.selected.indices[0]
+        selected_scan_id = scan_table_source.data["scan"][selected_index]
+        return det_data["scan"][selected_scan_id]
 
     def peak_pos_textinput_callback(_attr, _old, new):
         if new is not None and not peak_pos_textinput_lock:
-            sel_ind = scan_table_source.selected.indices[-1]
+            scan = _get_selected_scan()
-            scan_name = scan_table_source.data["scan"][sel_ind]
-            scan = det_data["scan"][scan_name]
 
             scan["num_of_peaks"] = 1
             peak_ind = (np.abs(scan["om"] - float(new))).argmin()
             scan["peak_indexes"] = np.array([peak_ind], dtype=np.int64)
             scan["peak_heights"] = np.array([scan["smooth_peaks"][peak_ind]])
             _update_table()
-            _update_plot(scan_name)
+            _update_plot(scan)
 
     peak_pos_textinput = TextInput(title="Peak position:", default_size=145)
     peak_pos_textinput.on_change("value", peak_pos_textinput_callback)
@@ -322,30 +353,8 @@ def create():
 
     fit_output_textinput = TextAreaInput(title="Fit results:", width=450, height=400)
 
-    def peakfind_all_button_callback():
+    def _get_peakfind_params():
-        for scan in det_data["scan"].values():
+        return dict(
-            pyzebra.ccl_findpeaks(
-                scan,
-                int_threshold=peak_int_ratio_spinner.value,
-                prominence=peak_prominence_spinner.value,
-                smooth=smooth_toggle.active,
-                window_size=window_size_spinner.value,
-                poly_order=poly_order_spinner.value,
-            )
-
-        _update_table()
-
-        sel_ind = scan_table_source.selected.indices[-1]
-        _update_plot(scan_table_source.data["scan"][sel_ind])
-
-    peakfind_all_button = Button(label="Peak Find All", button_type="primary", default_size=145)
-    peakfind_all_button.on_click(peakfind_all_button_callback)
-
-    def peakfind_button_callback():
-        sel_ind = scan_table_source.selected.indices[-1]
-        scan = scan_table_source.data["scan"][sel_ind]
-        pyzebra.ccl_findpeaks(
-            det_data["scan"][scan],
             int_threshold=peak_int_ratio_spinner.value,
             prominence=peak_prominence_spinner.value,
             smooth=smooth_toggle.active,
@@ -353,61 +362,29 @@ def create():
             poly_order=poly_order_spinner.value,
         )
 
+    def peakfind_all_button_callback():
+        peakfind_params = _get_peakfind_params()
+        for scan in det_data["scan"].values():
+            pyzebra.ccl_findpeaks(scan, **peakfind_params)
+
+        _update_table()
+        _update_plot(_get_selected_scan())
+
+    peakfind_all_button = Button(label="Peak Find All", button_type="primary", default_size=145)
+    peakfind_all_button.on_click(peakfind_all_button_callback)
+
+    def peakfind_button_callback():
+        scan = _get_selected_scan()
+        pyzebra.ccl_findpeaks(scan, **_get_peakfind_params())
+
         _update_table()
         _update_plot(scan)
 
     peakfind_button = Button(label="Peak Find Current", default_size=145)
     peakfind_button.on_click(peakfind_button_callback)
 
-    def fit_all_button_callback():
+    def _get_fit_params():
-        for scan in det_data["scan"].values():
+        return dict(
-            pyzebra.fitccl(
-                scan,
-                guess=[
-                    centre_guess.value,
-                    sigma_guess.value,
-                    ampl_guess.value,
-                    slope_guess.value,
-                    offset_guess.value,
-                ],
-                vary=[
-                    centre_vary.active,
-                    sigma_vary.active,
-                    ampl_vary.active,
-                    slope_vary.active,
-                    offset_vary.active,
-                ],
-                constraints_min=[
-                    centre_min.value,
-                    sigma_min.value,
-                    ampl_min.value,
-                    slope_min.value,
-                    offset_min.value,
-                ],
-                constraints_max=[
-                    centre_max.value,
-                    sigma_max.value,
-                    ampl_max.value,
-                    slope_max.value,
-                    offset_max.value,
-                ],
-                numfit_min=integ_from.value,
-                numfit_max=integ_to.value,
-            )
-
-        sel_ind = scan_table_source.selected.indices[-1]
-        _update_plot(scan_table_source.data["scan"][sel_ind])
-        _update_table()
-
-    fit_all_button = Button(label="Fit All", button_type="primary", default_size=145)
-    fit_all_button.on_click(fit_all_button_callback)
-
-    def fit_button_callback():
-        sel_ind = scan_table_source.selected.indices[-1]
-        scan = scan_table_source.data["scan"][sel_ind]
-
-        pyzebra.fitccl(
-            det_data["scan"][scan],
             guess=[
                 centre_guess.value,
                 sigma_guess.value,
@@ -438,8 +415,25 @@ def create():
             ],
             numfit_min=integ_from.value,
             numfit_max=integ_to.value,
+            binning=bin_size_spinner.value,
         )
 
+    def fit_all_button_callback():
+        fit_params = _get_fit_params()
+        for scan in det_data["scan"].values():
+            # fit_params are updated inplace within `fitccl`
+            pyzebra.fitccl(scan, **deepcopy(fit_params))
+
+        _update_plot(_get_selected_scan())
+        _update_table()
+
+    fit_all_button = Button(label="Fit All", button_type="primary", default_size=145)
+    fit_all_button.on_click(fit_all_button_callback)
+
+    def fit_button_callback():
+        scan = _get_selected_scan()
+        pyzebra.fitccl(scan, **_get_fit_params())
+
         _update_plot(scan)
         _update_table()
 
@@ -454,6 +448,10 @@ def create():
     )
     area_method_radiobutton.on_change("active", area_method_radiobutton_callback)
 
+    bin_size_spinner = Spinner(title="Bin size:", value=1, low=1, step=1, default_size=145)
+
+    lorentz_toggle = Toggle(label="Lorentz Correction", default_size=145)
+
     preview_output_textinput = TextAreaInput(title="Export file preview:", width=450, height=400)
 
     def preview_output_button_callback():
@@ -464,7 +462,11 @@ def create():
 
         with tempfile.TemporaryDirectory() as temp_dir:
             temp_file = temp_dir + "/temp"
-            pyzebra.export_comm(det_data, temp_file)
+            export_data = deepcopy(det_data)
+            for s, export in zip(scan_table_source.data["scan"], scan_table_source.data["export"]):
+                if not export:
+                    del export_data["scan"][s]
+            pyzebra.export_comm(export_data, temp_file, lorentz=lorentz_toggle.active)
 
             with open(f"{temp_file}{ext}") as f:
                 preview_output_textinput.value = f.read()
@@ -480,7 +482,11 @@ def create():
 
         with tempfile.TemporaryDirectory() as temp_dir:
             temp_file = temp_dir + "/temp"
-            pyzebra.export_comm(det_data, temp_file)
+            export_data = deepcopy(det_data)
+            for s, export in zip(scan_table_source.data["scan"], scan_table_source.data["export"]):
+                if not export:
+                    del export_data["scan"][s]
+            pyzebra.export_comm(export_data, temp_file, lorentz=lorentz_toggle.active)
 
             with open(f"{temp_file}{ext}") as f:
                 output_content = f.read()
@@ -530,6 +536,7 @@ def create():
         Spacer(width=20),
         column(
             row(integ_from, integ_to),
+            row(bin_size_spinner, column(Spacer(height=19), lorentz_toggle)),
             row(fitparam_reset_button, area_method_radiobutton),
             row(fit_button, fit_all_button),
         ),
@@ -538,9 +545,15 @@ def create():
     export_layout = column(preview_output_textinput, row(preview_output_button, save_button))
 
     upload_div = Div(text="Or upload .ccl file:")
+    append_upload_div = Div(text="append extra .ccl/.dat files:")
     tab_layout = column(
         row(proposal_textinput, ccl_file_select),
-        row(column(Spacer(height=5), upload_div), upload_button),
+        row(
+            column(Spacer(height=5), upload_div),
+            upload_button,
+            column(Spacer(height=5), append_upload_div),
+            append_upload_button,
+        ),
         row(scan_table, plot, Spacer(width=30), fit_output_textinput, export_layout),
         row(findpeak_controls, Spacer(width=30), fitpeak_controls),
     )

pyzebra/app/panel_hdf_anatric.py

@@ -21,6 +21,7 @@ from pyzebra.anatric import DATA_FACTORY_IMPLEMENTATION, REFLECTION_PRINTER_FORM
 
 
 def create():
+    doc = curdoc()
     config = pyzebra.AnatricConfig()
 
     def _load_config_file(file):
@@ -345,7 +346,7 @@ def create():
         with tempfile.TemporaryDirectory() as temp_dir:
             temp_file = temp_dir + "/temp.xml"
             config.save_as(temp_file)
-            pyzebra.anatric(temp_file)
+            pyzebra.anatric(temp_file, anatric_path=doc.anatric_path)
 
             with open(config.logfile) as f_log:
                 output_log.value = f_log.read()
@@ -404,6 +405,6 @@ def create():
         with open("debug.xml") as f_config:
             output_config.value = f_config.read()
 
-    curdoc().add_periodic_callback(update_config, 1000)
+    doc.add_periodic_callback(update_config, 1000)
 
     return Panel(child=tab_layout, title="hdf anatric")

pyzebra/app/panel_hdf_viewer.py

@@ -74,8 +74,8 @@ def create():
         image_source.data.update(image=[current_image])
 
         if auto_toggle.active:
-            im_max = int(np.max(current_image))
+            im_min = np.min(current_image)
-            im_min = int(np.min(current_image))
+            im_max = np.max(current_image)
 
             display_min_spinner.value = im_min
             display_max_spinner.value = im_max
@@ -83,8 +83,15 @@ def create():
             image_glyph.color_mapper.low = im_min
             image_glyph.color_mapper.high = im_max
 
-        magnetic_field_spinner.value = det_data["magnetic_field"][index]
+        if "magnetic_field" in det_data:
-        temperature_spinner.value = det_data["temperature"][index]
+            magnetic_field_spinner.value = det_data["magnetic_field"][index]
+        else:
+            magnetic_field_spinner.value = None
+
+        if "temperature" in det_data:
+            temperature_spinner.value = det_data["temperature"][index]
+        else:
+            temperature_spinner.value = None
 
         gamma, nu = calculate_pol(det_data, index)
         omega = np.ones((IMAGE_H, IMAGE_W)) * det_data["rot_angle"][index]
@@ -99,6 +106,18 @@ def create():
         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])
 
+        if proj_auto_toggle.active:
+            im_min = min(np.min(overview_x), np.min(overview_y))
+            im_max = max(np.max(overview_x), np.max(overview_y))
+
+            proj_display_min_spinner.value = im_min
+            proj_display_max_spinner.value = im_max
+
+            overview_plot_x_image_glyph.color_mapper.low = im_min
+            overview_plot_y_image_glyph.color_mapper.low = im_min
+            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"
@@ -388,7 +407,6 @@ def create():
     radio_button_group = RadioButtonGroup(labels=["nb", "nb_bi"], active=0)
 
     STEP = 1
-
     # ---- colormap auto toggle button
     def auto_toggle_callback(state):
         if state:
@@ -400,7 +418,9 @@ def create():
 
         update_image()
 
-    auto_toggle = Toggle(label="Auto Range", active=True, button_type="default", default_size=145)
+    auto_toggle = Toggle(
+        label="Main Auto Range", active=True, button_type="default", default_size=125
+    )
     auto_toggle.on_click(auto_toggle_callback)
 
     # ---- colormap display max value
@@ -409,12 +429,12 @@ def create():
         image_glyph.color_mapper.high = new_value
 
     display_max_spinner = Spinner(
-        title="Maximal Display Value:",
+        title="Max Value:",
         low=0 + STEP,
         value=1,
         step=STEP,
         disabled=auto_toggle.active,
-        default_size=145,
+        default_size=80,
     )
     display_max_spinner.on_change("value", display_max_spinner_callback)
 
@@ -424,15 +444,66 @@ def create():
         image_glyph.color_mapper.low = new_value
 
     display_min_spinner = Spinner(
-        title="Minimal Display Value:",
+        title="Min Value:",
+        low=0,
         high=1 - STEP,
         value=0,
         step=STEP,
         disabled=auto_toggle.active,
-        default_size=145,
+        default_size=80,
     )
     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):
+        if state:
+            proj_display_min_spinner.disabled = True
+            proj_display_max_spinner.disabled = True
+        else:
+            proj_display_min_spinner.disabled = False
+            proj_display_max_spinner.disabled = False
+
+        update_overview_plot()
+
+    proj_auto_toggle = Toggle(
+        label="Proj Auto Range", active=True, button_type="default", default_size=125
+    )
+    proj_auto_toggle.on_click(proj_auto_toggle_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,
+    )
+    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,
+    )
+    proj_display_min_spinner.on_change("value", proj_display_min_spinner_callback)
+
     def hkl_button_callback():
         index = index_spinner.value
         setup_type = "nb_bi" if radio_button_group.active else "nb"
@@ -474,8 +545,13 @@ def create():
     # Final layout
     layout_image = column(gridplot([[proj_v, None], [plot, proj_h]], merge_tools=False))
     colormap_layout = column(
-        row(colormap, column(Spacer(height=19), auto_toggle)),
+        row(colormap),
-        row(display_max_spinner, display_min_spinner),
+        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,
+        ),
     )
     hkl_layout = column(radio_button_group, hkl_button)
     params_layout = row(magnetic_field_spinner, temperature_spinner)

pyzebra/ccl_dict_operation.py

@@ -1,513 +0,0 @@
-import numpy as np
-import uncertainties as u
-
-from .fit2 import create_uncertanities
-
-
-def add_dict(dict1, dict2):
-    """adds two dictionaries, meta of the new is saved as meata+original_filename and
-    measurements are shifted to continue with numbering of first dict
-    :arg dict1 : dictionarry to add to
-    :arg dict2 : dictionarry from which to take the measurements
-    :return dict1 : combined dictionary
-    Note: dict1 must be made from ccl, otherwise we would have to change the structure of loaded
-    dat file"""
-    max_measurement_dict1 = max([int(str(keys)[1:]) for keys in dict1["scan"]])
-    if dict2["meta"]["data_type"] == ".ccl":
-        new_filenames = [
-            "M" + str(x + max_measurement_dict1)
-            for x in [int(str(keys)[1:]) for keys in dict2["scan"]]
-        ]
-        new_meta_name = "meta" + str(dict2["meta"]["original_filename"])
-        if new_meta_name not in dict1:
-            for keys, name in zip(dict2["scan"], new_filenames):
-                dict2["scan"][keys]["file_of_origin"] = str(dict2["meta"]["original_filename"])
-                dict1["scan"][name] = dict2["scan"][keys]
-
-            dict1[new_meta_name] = dict2["meta"]
-
-        else:
-            raise KeyError(
-                str(
-                    "The file %s has alredy been added to %s"
-                    % (dict2["meta"]["original_filename"], dict1["meta"]["original_filename"])
-                )
-            )
-    elif dict2["meta"]["data_type"] == ".dat":
-        d = {}
-        new_name = "M" + str(max_measurement_dict1 + 1)
-        hkl = dict2["meta"]["title"]
-        d["h_index"] = float(hkl.split()[-3])
-        d["k_index"] = float(hkl.split()[-2])
-        d["l_index"] = float(hkl.split()[-1])
-        d["number_of_measurements"] = len(dict2["scan"]["NP"])
-        d["om"] = dict2["scan"]["om"]
-        d["Counts"] = dict2["scan"]["Counts"]
-        d["monitor"] = dict2["scan"]["Monitor1"][0]
-        d["temperature"] = dict2["meta"]["temp"]
-        d["mag_field"] = dict2["meta"]["mf"]
-        d["omega_angle"] = dict2["meta"]["omega"]
-        dict1["scan"][new_name] = d
-        print(hkl.split())
-        for keys in d:
-            print(keys)
-
-        print("s")
-
-    return dict1
-
-
-def auto(dict):
-    """takes just unique tuples from all tuples in dictionary returend by scan_dict
-    intendet for automatic merge if you doesent want to specify what scans to merge together
-    args: dict - dictionary from scan_dict function
-    :return dict - dict without repetitions"""
-    for keys in dict:
-        tuple_list = dict[keys]
-        new = list()
-        for i in range(len(tuple_list)):
-            if tuple_list[0][0] == tuple_list[i][0]:
-                new.append(tuple_list[i])
-        dict[keys] = new
-    return dict
-
-
-def scan_dict(dict):
-    """scans dictionary for duplicate hkl indexes
-    :arg dict : dictionary to scan
-    :return  dictionary with matching scans, if there are none, the dict is empty
-    note: can be checked by "not d", true if empty
-    """
-
-    d = {}
-    for i in dict["scan"]:
-        for j in dict["scan"]:
-            if dict["scan"][str(i)] != dict["scan"][str(j)]:
-                itup = (
-                    dict["scan"][str(i)]["h_index"],
-                    dict["scan"][str(i)]["k_index"],
-                    dict["scan"][str(i)]["l_index"],
-                )
-                jtup = (
-                    dict["scan"][str(j)]["h_index"],
-                    dict["scan"][str(j)]["k_index"],
-                    dict["scan"][str(j)]["l_index"],
-                )
-                if itup != jtup:
-                    pass
-                else:
-
-                    if str(itup) not in d:
-                        d[str(itup)] = list()
-                        d[str(itup)].append((i, j))
-                    else:
-                        d[str(itup)].append((i, j))
-            else:
-                continue
-    return d
-
-
-def compare_hkl(dict1, dict2):
-    """Compares two dictionaries based on hkl indexes and return dictionary with str(h k l) as
-    key and tuple with keys to same scan in dict1 and dict2
-    :arg dict1 : first dictionary
-    :arg dict2 : second dictionary
-    :return d : dict with matches
-    example of one key: '0.0 0.0 -1.0 : ('M1', 'M9')' meaning that 001 hkl scan is M1 in
-    first dict and M9 in second"""
-    d = {}
-    dupl = 0
-    for keys in dict1["scan"]:
-        for key in dict2["scan"]:
-            if (
-                dict1["scan"][str(keys)]["h_index"] == dict2["scan"][str(key)]["h_index"]
-                and dict1["scan"][str(keys)]["k_index"] == dict2["scan"][str(key)]["k_index"]
-                and dict1["scan"][str(keys)]["l_index"] == dict2["scan"][str(key)]["l_index"]
-            ):
-
-                if (
-                    str(
-                        (
-                            str(dict1["scan"][str(keys)]["h_index"])
-                            + " "
-                            + str(dict1["scan"][str(keys)]["k_index"])
-                            + " "
-                            + str(dict1["scan"][str(keys)]["l_index"])
-                        )
-                    )
-                    not in d
-                ):
-                    d[
-                        str(
-                            str(dict1["scan"][str(keys)]["h_index"])
-                            + " "
-                            + str(dict1["scan"][str(keys)]["k_index"])
-                            + " "
-                            + str(dict1["scan"][str(keys)]["l_index"])
-                        )
-                    ] = (str(keys), str(key))
-                else:
-                    dupl = dupl + 1
-                    d[
-                        str(
-                            str(dict1["scan"][str(keys)]["h_index"])
-                            + " "
-                            + str(dict1["scan"][str(keys)]["k_index"])
-                            + " "
-                            + str(dict1["scan"][str(keys)]["l_index"])
-                            + "_dupl"
-                            + str(dupl)
-                        )
-                    ] = (str(keys), str(key))
-            else:
-                continue
-
-    return d
-
-
-def create_tuples(x, y, y_err):
-    """creates tuples for sorting and merginng of the data
-    Counts need to be normalized to monitor before"""
-    t = list()
-    for i in range(len(x)):
-        tup = (x[i], y[i], y_err[i])
-        t.append(tup)
-    return t
-
-
-def normalize(dict, key, monitor):
-    """Normalizes the scan to monitor, checks if sigma exists, otherwise creates it
-    :arg dict : dictionary to from which to tkae the scan
-    :arg key : which scan to normalize from dict1
-    :arg monitor : final monitor
-    :return counts - normalized counts
-    :return sigma - normalized sigma"""
-
-    counts = np.array(dict["scan"][key]["Counts"])
-    sigma = np.sqrt(counts) if "sigma" not in dict["scan"][key] else dict["scan"][key]["sigma"]
-    monitor_ratio = monitor / dict["scan"][key]["monitor"]
-    scaled_counts = counts * monitor_ratio
-    scaled_sigma = np.array(sigma) * monitor_ratio
-
-    return scaled_counts, scaled_sigma
-
-
-def merge(dict1, dict2, keys, auto=True, monitor=100000):
-    """merges the two tuples and sorts them, if om value is same, Counts value is average
-    averaging is propagated into sigma if dict1 == dict2, key[1] is deleted after merging
-    :arg dict1 : dictionary to which scan will be merged
-    :arg dict2 : dictionary from which scan will be merged
-    :arg keys : tuple with key to dict1 and dict2
-    :arg auto : if true, when monitors are same, does not change it, if flase, takes monitor always
-    :arg monitor : final monitor after merging
-    note: dict1 and dict2 can be same dict
-    :return dict1 with merged scan"""
-    if auto:
-        if dict1["scan"][keys[0]]["monitor"] == dict2["scan"][keys[1]]["monitor"]:
-            monitor = dict1["scan"][keys[0]]["monitor"]
-
-    # load om and Counts
-    x1, x2 = dict1["scan"][keys[0]]["om"], dict2["scan"][keys[1]]["om"]
-    cor_y1, y_err1 = normalize(dict1, keys[0], monitor=monitor)
-    cor_y2, y_err2 = normalize(dict2, keys[1], monitor=monitor)
-    # creates touples (om, Counts, sigma) for sorting and further processing
-    tuple_list = create_tuples(x1, cor_y1, y_err1) + create_tuples(x2, cor_y2, y_err2)
-    # Sort the list on om and add 0 0 0 tuple to the last position
-    sorted_t = sorted(tuple_list, key=lambda tup: tup[0])
-    sorted_t.append((0, 0, 0))
-    om, Counts, sigma = [], [], []
-    seen = list()
-    for i in range(len(sorted_t) - 1):
-        if sorted_t[i][0] not in seen:
-            if sorted_t[i][0] != sorted_t[i + 1][0]:
-                om = np.append(om, sorted_t[i][0])
-                Counts = np.append(Counts, sorted_t[i][1])
-                sigma = np.append(sigma, sorted_t[i][2])
-            else:
-                om = np.append(om, sorted_t[i][0])
-                counts1, counts2 = sorted_t[i][1], sorted_t[i + 1][1]
-                sigma1, sigma2 = sorted_t[i][2], sorted_t[i + 1][2]
-                count_err1 = u.ufloat(counts1, sigma1)
-                count_err2 = u.ufloat(counts2, sigma2)
-                avg = (count_err1 + count_err2) / 2
-                Counts = np.append(Counts, avg.n)
-                sigma = np.append(sigma, avg.s)
-                seen.append(sorted_t[i][0])
-        else:
-            continue
-
-    if dict1 == dict2:
-        del dict1["scan"][keys[1]]
-
-    note = (
-        f"This scan was merged with scan {keys[1]} from "
-        f'file {dict2["meta"]["original_filename"]} \n'
-    )
-    if "notes" not in dict1["scan"][str(keys[0])]:
-        dict1["scan"][str(keys[0])]["notes"] = note
-    else:
-        dict1["scan"][str(keys[0])]["notes"] += note
-
-    dict1["scan"][keys[0]]["om"] = om
-    dict1["scan"][keys[0]]["Counts"] = Counts
-    dict1["scan"][keys[0]]["sigma"] = sigma
-    dict1["scan"][keys[0]]["monitor"] = monitor
-    print("merging done")
-    return dict1
-
-
-def substract_measurement(dict1, dict2, keys, auto=True, monitor=100000):
-    """Substracts two scan (scan key2 from dict2 from measurent key1 in dict1), expects om to be same
-    :arg dict1 : dictionary to which scan will be merged
-    :arg dict2 : dictionary from which scan will be merged
-    :arg keys : tuple with key to dict1 and dict2
-    :arg auto : if true, when monitors are same, does not change it, if flase, takes monitor always
-    :arg monitor : final monitor after merging
-    :returns d : dict1 with substracted Counts from  dict2 and sigma that comes from the substraction"""
-
-    if len(dict1["scan"][keys[0]]["om"]) != len(dict2["scan"][keys[1]]["om"]):
-        raise ValueError("Omegas have different lengths, cannot be substracted")
-
-    if auto:
-        if dict1["scan"][keys[0]]["monitor"] == dict2["scan"][keys[1]]["monitor"]:
-            monitor = dict1["scan"][keys[0]]["monitor"]
-
-    cor_y1, y_err1 = normalize(dict1, keys[0], monitor=monitor)
-    cor_y2, y_err2 = normalize(dict2, keys[1], monitor=monitor)
-
-    dict1_count_err = create_uncertanities(cor_y1, y_err1)
-    dict2_count_err = create_uncertanities(cor_y2, y_err2)
-
-    res = np.subtract(dict1_count_err, dict2_count_err)
-
-    res_nom = []
-    res_err = []
-    for k in range(len(res)):
-        res_nom = np.append(res_nom, res[k].n)
-        res_err = np.append(res_err, res[k].s)
-
-    if len([num for num in res_nom if num < 0]) >= 0.3 * len(res_nom):
-        print(
-            f"Warning! percentage of negative numbers in scan subsracted {keys[0]} is "
-            f"{len([num for num in res_nom if num < 0]) / len(res_nom)}"
-        )
-
-    dict1["scan"][str(keys[0])]["Counts"] = res_nom
-    dict1["scan"][str(keys[0])]["sigma"] = res_err
-    dict1["scan"][str(keys[0])]["monitor"] = monitor
-    note = (
-        f'Scan {keys[1]} from file {dict2["meta"]["original_filename"]} '
-        f"was substracted from this scan \n"
-    )
-    if "notes" not in dict1["scan"][str(keys[0])]:
-        dict1["scan"][str(keys[0])]["notes"] = note
-    else:
-        dict1["scan"][str(keys[0])]["notes"] += note
-    return dict1
-
-
-def compare_dict(dict1, dict2):
-    """takes two ccl dictionaries and compare different values for each key
-    :arg dict1 : dictionary 1 (ccl)
-    :arg dict2 : dictionary 2 (ccl)
-    :returns warning : dictionary with keys from primary files (if they differ) with
-    information of how many scan differ and which ones differ
-    :returns report_string string comparing all different values respecively of measurements"""
-
-    if dict1["meta"]["data_type"] != dict2["meta"]["data_type"]:
-        print("select two dicts")
-        return
-    S = []
-    conflicts = {}
-    warnings = {}
-
-    comp = compare_hkl(dict1, dict2)
-    d1 = scan_dict(dict1)
-    d2 = scan_dict(dict2)
-    if not d1:
-        S.append("There are no duplicates in %s (dict1) \n" % dict1["meta"]["original_filename"])
-    else:
-        S.append(
-            "There are %d duplicates in %s (dict1) \n"
-            % (len(d1), dict1["meta"]["original_filename"])
-        )
-        warnings["Duplicates in dict1"] = list()
-        for keys in d1:
-            S.append("Measurements %s with hkl %s \n" % (d1[keys], keys))
-            warnings["Duplicates in dict1"].append(d1[keys])
-    if not d2:
-        S.append("There are no duplicates in %s (dict2) \n" % dict2["meta"]["original_filename"])
-    else:
-        S.append(
-            "There are %d duplicates in %s (dict2) \n"
-            % (len(d2), dict2["meta"]["original_filename"])
-        )
-        warnings["Duplicates in dict2"] = list()
-        for keys in d2:
-            S.append("Measurements %s with hkl %s \n" % (d2[keys], keys))
-            warnings["Duplicates in dict2"].append(d2[keys])
-
-    # compare meta
-    S.append("Different values in meta: \n")
-    different_meta = {
-        k: dict1["meta"][k]
-        for k in dict1["meta"]
-        if k in dict2["meta"] and dict1["meta"][k] != dict2["meta"][k]
-    }
-    exlude_meta_set = ["original_filename", "date", "title"]
-    for keys in different_meta:
-        if keys in exlude_meta_set:
-            continue
-        else:
-            if keys not in conflicts:
-                conflicts[keys] = 1
-            else:
-                conflicts[keys] = conflicts[keys] + 1
-
-            S.append("   Different values in %s \n" % str(keys))
-            S.append("           dict1: %s \n" % str(dict1["meta"][str(keys)]))
-            S.append("           dict2: %s \n" % str(dict2["meta"][str(keys)]))
-
-    # compare Measurements
-    S.append(
-        "Number of measurements in %s = %s \n"
-        % (dict1["meta"]["original_filename"], len(dict1["scan"]))
-    )
-    S.append(
-        "Number of measurements in %s = %s \n"
-        % (dict2["meta"]["original_filename"], len(dict2["scan"]))
-    )
-    S.append("Different values in Measurements:\n")
-    select_set = ["om", "Counts", "sigma"]
-    exlude_set = ["time", "Counts", "date", "notes"]
-    for keys1 in comp:
-        for key2 in dict1["scan"][str(comp[str(keys1)][0])]:
-            if key2 in exlude_set:
-                continue
-            if key2 not in select_set:
-                try:
-                    if (
-                        dict1["scan"][comp[str(keys1)][0]][str(key2)]
-                        != dict2["scan"][str(comp[str(keys1)][1])][str(key2)]
-                    ):
-                        S.append(
-                            "Scan value "
-                            "%s"
-                            ", with hkl %s differs in meausrements %s and %s \n"
-                            % (key2, keys1, comp[str(keys1)][0], comp[str(keys1)][1])
-                        )
-                        S.append(
-                            "     dict1:   %s \n"
-                            % str(dict1["scan"][comp[str(keys1)][0]][str(key2)])
-                        )
-                        S.append(
-                            "     dict2:   %s \n"
-                            % str(dict2["scan"][comp[str(keys1)][1]][str(key2)])
-                        )
-                        if key2 not in conflicts:
-                            conflicts[key2] = {}
-                            conflicts[key2]["amount"] = 1
-                            conflicts[key2]["scan"] = str(comp[str(keys1)])
-                        else:
-
-                            conflicts[key2]["amount"] = conflicts[key2]["amount"] + 1
-                            conflicts[key2]["scan"] = (
-                                conflicts[key2]["scan"] + " " + (str(comp[str(keys1)]))
-                            )
-                except KeyError as e:
-                    print("Missing keys, some files were probably merged or substracted")
-                    print(e.args)
-
-            else:
-                try:
-                    comparison = list(dict1["scan"][comp[str(keys1)][0]][str(key2)]) == list(
-                        dict2["scan"][comp[str(keys1)][1]][str(key2)]
-                    )
-                    if len(list(dict1["scan"][comp[str(keys1)][0]][str(key2)])) != len(
-                        list(dict2["scan"][comp[str(keys1)][1]][str(key2)])
-                    ):
-                        if str("different length of %s" % key2) not in warnings:
-                            warnings[str("different length of %s" % key2)] = list()
-                            warnings[str("different length of %s" % key2)].append(
-                                (str(comp[keys1][0]), str(comp[keys1][1]))
-                            )
-                        else:
-                            warnings[str("different length of %s" % key2)].append(
-                                (str(comp[keys1][0]), str(comp[keys1][1]))
-                            )
-                    if not comparison:
-                        S.append(
-                            "Scan value "
-                            "%s"
-                            " differs in scan %s and %s \n"
-                            % (key2, comp[str(keys1)][0], comp[str(keys1)][1])
-                        )
-                        S.append(
-                            "       dict1:   %s \n"
-                            % str(list(dict1["scan"][comp[str(keys1)][0]][str(key2)]))
-                        )
-                        S.append(
-                            "       dict2:   %s \n"
-                            % str(list(dict2["scan"][comp[str(keys1)][1]][str(key2)]))
-                        )
-                        if key2 not in conflicts:
-                            conflicts[key2] = {}
-                            conflicts[key2]["amount"] = 1
-                            conflicts[key2]["scan"] = str(comp[str(keys1)])
-                        else:
-                            conflicts[key2]["amount"] = conflicts[key2]["amount"] + 1
-                            conflicts[key2]["scan"] = (
-                                conflicts[key2]["scan"] + " " + (str(comp[str(keys1)]))
-                            )
-                except KeyError as e:
-                    print("Missing keys, some files were probably merged or substracted")
-                    print(e.args)
-
-    for keys in conflicts:
-        try:
-            conflicts[str(keys)]["scan"] = conflicts[str(keys)]["scan"].split(" ")
-        except:
-            continue
-    report_string = "".join(S)
-    return warnings, conflicts, report_string
-
-
-def guess_next(dict1, dict2, comp):
-    """iterates thorough the scans and tries to decide if the scans should be
-    substracted or merged"""
-    threshold = 0.05
-    for keys in comp:
-        if (
-            abs(
-                (
-                    dict1["scan"][str(comp[keys][0])]["temperature"]
-                    - dict2["scan"][str(comp[keys][1])]["temperature"]
-                )
-                / dict2["scan"][str(comp[keys][1])]["temperature"]
-            )
-            < threshold
-            and abs(
-                (
-                    dict1["scan"][str(comp[keys][0])]["mag_field"]
-                    - dict2["scan"][str(comp[keys][1])]["mag_field"]
-                )
-                / dict2["scan"][str(comp[keys][1])]["mag_field"]
-            )
-            < threshold
-        ):
-            comp[keys] = comp[keys] + tuple("m")
-        else:
-            comp[keys] = comp[keys] + tuple("s")
-
-    return comp
-
-
-def process_dict(dict1, dict2, comp):
-    """substracts or merges scans, guess_next function must run first """
-    for keys in comp:
-        if comp[keys][2] == "s":
-            substract_measurement(dict1, dict2, comp[keys])
-        elif comp[keys][2] == "m":
-            merge(dict1, dict2, comp[keys])
-
-    return dict1

pyzebra/ccl_findpeaks.py

@@ -5,7 +5,13 @@ from scipy.signal import savgol_filter
 
 
 def ccl_findpeaks(
-    scan, int_threshold=0.8, prominence=50, smooth=False, window_size=7, poly_order=3
+    scan,
+    int_threshold=0.8,
+    prominence=50,
+    smooth=False,
+    window_size=7,
+    poly_order=3,
+    variable="om",
 ):
 
     """function iterates through the dictionary created by load_cclv2 and locates peaks for each scan
@@ -54,7 +60,7 @@ def ccl_findpeaks(
         prominence = 50
         print("Invalid value for prominence, select positive number, new value set to:", prominence)
 
-    omega = scan["om"]
+    omega = scan[variable]
     counts = np.array(scan["Counts"])
     if smooth:
         itp = interp1d(omega, counts, kind="linear")

pyzebra/ccl_io.py

@@ -1,7 +1,6 @@
 import os
 import re
 from collections import defaultdict
-from decimal import Decimal
 
 import numpy as np
 
@@ -20,6 +19,7 @@ META_VARS_STR = (
     "proposal_email",
     "detectorDistance",
 )
+
 META_VARS_FLOAT = (
     "omega",
     "mf",
@@ -58,30 +58,29 @@ META_VARS_FLOAT = (
 META_UB_MATRIX = ("ub1j", "ub2j", "ub3j")
 
 CCL_FIRST_LINE = (
-    # the first element is `scan_number`, which we don't save to metadata
+    ("scan_number", int),
     ("h_index", float),
     ("k_index", float),
     ("l_index", float),
 )
 
-CCL_FIRST_LINE_BI = (
+CCL_ANGLES = {
-    *CCL_FIRST_LINE,
+    "bi": (
-    ("twotheta_angle", float),
+        ("twotheta_angle", float),
-    ("omega_angle", float),
+        ("omega_angle", float),
-    ("chi_angle", float),
+        ("chi_angle", float),
-    ("phi_angle", float),
+        ("phi_angle", float),
-)
+    ),
-
+    "nb": (
-CCL_FIRST_LINE_NB = (
+        ("gamma_angle", float),
-    *CCL_FIRST_LINE,
+        ("omega_angle", float),
-    ("gamma_angle", float),
+        ("nu_angle", float),
-    ("omega_angle", float),
+        ("unkwn_angle", float),
-    ("nu_angle", float),
+    ),
-    ("unkwn_angle", float),
+}
-)
 
 CCL_SECOND_LINE = (
-    ("number_of_measurements", int),
+    ("n_points", int),
     ("angle_step", float),
     ("monitor", float),
     ("temperature", float),
@@ -132,50 +131,34 @@ def parse_1D(fileobj, data_type):
     # read data
     scan = {}
     if data_type == ".ccl":
-        decimal = list()
+        ccl_first_line = (*CCL_FIRST_LINE, *CCL_ANGLES[metadata["zebra_mode"]])
-
-        if metadata["zebra_mode"] == "bi":
-            ccl_first_line = CCL_FIRST_LINE_BI
-        elif metadata["zebra_mode"] == "nb":
-            ccl_first_line = CCL_FIRST_LINE_NB
         ccl_second_line = CCL_SECOND_LINE
 
         for line in fileobj:
             d = {}
 
             # first line
-            scan_number, *params = line.split()
+            for param, (param_name, param_type) in zip(line.split(), ccl_first_line):
-            for param, (param_name, param_type) in zip(params, ccl_first_line):
                 d[param_name] = param_type(param)
 
-            decimal.append(bool(Decimal(d["h_index"]) % 1 == 0))
-            decimal.append(bool(Decimal(d["k_index"]) % 1 == 0))
-            decimal.append(bool(Decimal(d["l_index"]) % 1 == 0))
-
             # second line
             next_line = next(fileobj)
-            params = next_line.split()
+            for param, (param_name, param_type) in zip(next_line.split(), ccl_second_line):
-            for param, (param_name, param_type) in zip(params, ccl_second_line):
                 d[param_name] = param_type(param)
 
             d["om"] = np.linspace(
-                d["omega_angle"] - (d["number_of_measurements"] / 2) * d["angle_step"],
+                d["omega_angle"] - (d["n_points"] / 2) * d["angle_step"],
-                d["omega_angle"] + (d["number_of_measurements"] / 2) * d["angle_step"],
+                d["omega_angle"] + (d["n_points"] / 2) * d["angle_step"],
-                d["number_of_measurements"],
+                d["n_points"],
             )
 
             # subsequent lines with counts
             counts = []
-            while len(counts) < d["number_of_measurements"]:
+            while len(counts) < d["n_points"]:
                 counts.extend(map(int, next(fileobj).split()))
             d["Counts"] = counts
 
-            scan[int(scan_number)] = d
+            scan[d["scan_number"]] = d
-
-            if all(decimal):
-                metadata["indices"] = "hkl"
-            else:
-                metadata["indices"] = "real"
 
     elif data_type == ".dat":
         # skip the first 2 rows, the third row contans the column names
@@ -200,9 +183,13 @@ def parse_1D(fileobj, data_type):
             print("seems hkl is not in title")
 
         data_cols["temperature"] = metadata["temp"]
-        data_cols["mag_field"] = metadata["mf"]
+        try:
+            data_cols["mag_field"] = metadata["mf"]
+        except KeyError:
+            print("Mag_field not present in dat file")
+
         data_cols["omega_angle"] = metadata["omega"]
-        data_cols["number_of_measurements"] = len(data_cols["om"])
+        data_cols["n_points"] = len(data_cols["om"])
         data_cols["monitor"] = data_cols["Monitor1"][0]
         data_cols["twotheta_angle"] = metadata["2-theta"]
         data_cols["chi_angle"] = metadata["chi"]
@@ -215,7 +202,69 @@ def parse_1D(fileobj, data_type):
         print("Unknown file extention")
 
     # utility information
+    if all(
+        s["h_index"].is_integer() and s["k_index"].is_integer() and s["l_index"].is_integer()
+        for s in scan.values()
+    ):
+        metadata["indices"] = "hkl"
+    else:
+        metadata["indices"] = "real"
+
     metadata["data_type"] = data_type
     metadata["area_method"] = "fit"
 
     return {"meta": metadata, "scan": scan}
+
+
+def export_comm(data, path, lorentz=False):
+    """exports data in the *.comm format
+    :param lorentz: perform Lorentz correction
+    :param path: path to file + name
+    :arg data - data to export, is dict after peak fitting
+
+    """
+    zebra_mode = data["meta"]["zebra_mode"]
+    if data["meta"]["indices"] == "hkl":
+        extension = ".comm"
+        padding = [6, 4]
+    elif data["meta"]["indices"] == "real":
+        extension = ".incomm"
+        padding = [4, 6]
+
+    with open(str(path + extension), "w") as out_file:
+        for key, scan in data["scan"].items():
+            if "fit" not in scan:
+                print("Scan skipped - no fit value for:", key)
+                continue
+
+            scan_str = f"{key:>{padding[0]}}"
+            h_str = f'{int(scan["h_index"]):{padding[1]}}'
+            k_str = f'{int(scan["k_index"]):{padding[1]}}'
+            l_str = f'{int(scan["l_index"]):{padding[1]}}'
+
+            if data["meta"]["area_method"] == "fit":
+                area = scan["fit"]["fit_area"].n
+                sigma_str = f'{scan["fit"]["fit_area"].s:>10.2f}'
+            elif data["meta"]["area_method"] == "integ":
+                area = scan["fit"]["int_area"].n
+                sigma_str = f'{scan["fit"]["int_area"].s:>10.2f}'
+
+            # apply lorentz correction to area
+            if lorentz:
+                if zebra_mode == "bi":
+                    twotheta_angle = np.deg2rad(scan["twotheta_angle"])
+                    corr_factor = np.sin(twotheta_angle)
+                elif zebra_mode == "nb":
+                    gamma_angle = np.deg2rad(scan["gamma_angle"])
+                    nu_angle = np.deg2rad(scan["nu_angle"])
+                    corr_factor = np.sin(gamma_angle) * np.cos(nu_angle)
+
+                area = np.abs(area * corr_factor)
+
+            area_str = f"{area:>10.2f}"
+
+            ang_str = ""
+            for angle, _ in CCL_ANGLES[zebra_mode]:
+                ang_str = ang_str + f"{scan[angle]:8}"
+
+            out_file.write(scan_str + h_str + k_str + l_str + area_str + sigma_str + ang_str + "\n")

pyzebra/cli.py

@@ -6,6 +6,8 @@ from bokeh.application.application import Application
 from bokeh.application.handlers import ScriptHandler
 from bokeh.server.server import Server
 
+from pyzebra.app.handler import PyzebraHandler
+
 logging.basicConfig(format="%(asctime)s %(message)s", level=logging.INFO)
 logger = logging.getLogger(__name__)
 
@@ -35,6 +37,13 @@ def main():
         help="hostname that can connect to the server websocket",
     )
 
+    parser.add_argument(
+        "--anatric-path",
+        type=str,
+        default="/afs/psi.ch/project/sinq/rhel7/bin/anatric",
+        help="path to anatric executable",
+    )
+
     parser.add_argument(
         "--args",
         nargs=argparse.REMAINDER,
@@ -46,9 +55,10 @@ def main():
 
     logger.info(app_path)
 
+    pyzebra_handler = PyzebraHandler(args.anatric_path)
     handler = ScriptHandler(filename=app_path, argv=args.args)
     server = Server(
-        {"/": Application(handler)},
+        {"/": Application(pyzebra_handler, handler)},
         port=args.port,
         allow_websocket_origin=args.allow_websocket_origin,
     )

pyzebra/comm_export.py

@@ -1,80 +0,0 @@
-import numpy as np
-
-
-def correction(value, lorentz=True, zebra_mode="--", ang1=0, ang2=0):
-    if lorentz is False:
-        return value
-    else:
-        if zebra_mode == "bi":
-            corr_value = np.abs(value * np.sin(ang1))
-            return corr_value
-        elif zebra_mode == "nb":
-            corr_value = np.abs(value * np.sin(ang1) * np.cos(ang2))
-            return corr_value
-
-
-def export_comm(data, path, lorentz=False):
-    """exports data in the *.comm format
-    :param lorentz: perform Lorentz correction
-    :param path: path to file + name
-    :arg data - data to export, is dict after peak fitting
-
-    """
-    zebra_mode = data["meta"]["zebra_mode"]
-    align = ">"
-    if data["meta"]["indices"] == "hkl":
-        extension = ".comm"
-        padding = [6, 4, 10, 8]
-    elif data["meta"]["indices"] == "real":
-        extension = ".incomm"
-        padding = [4, 6, 10, 8]
-
-    with open(str(path + extension), "w") as out_file:
-        for key, scan in data["scan"].items():
-            if "fit" not in scan:
-                print("Scan skipped - no fit value for:", key)
-                continue
-            scan_number_str = f"{key:{align}{padding[0]}}"
-            h_str = f'{int(scan["h_index"]):{padding[1]}}'
-            k_str = f'{int(scan["k_index"]):{padding[1]}}'
-            l_str = f'{int(scan["l_index"]):{padding[1]}}'
-            if data["meta"]["area_method"] == "fit":
-                area = float(scan["fit"]["fit_area"].n)
-                sigma_str = (
-                    f'{"{:8.2f}".format(float(scan["fit"]["fit_area"].s)):{align}{padding[2]}}'
-                )
-            elif data["meta"]["area_method"] == "integ":
-                area = float(scan["fit"]["int_area"].n)
-                sigma_str = (
-                    f'{"{:8.2f}".format(float(scan["fit"]["int_area"].s)):{align}{padding[2]}}'
-                )
-
-            if zebra_mode == "bi":
-                area = correction(area, lorentz, zebra_mode, scan["twotheta_angle"])
-                int_str = f'{"{:8.2f}".format(area):{align}{padding[2]}}'
-                angle_str1 = f'{scan["twotheta_angle"]:{padding[3]}}'
-                angle_str2 = f'{scan["omega_angle"]:{padding[3]}}'
-                angle_str3 = f'{scan["chi_angle"]:{padding[3]}}'
-                angle_str4 = f'{scan["phi_angle"]:{padding[3]}}'
-            elif zebra_mode == "nb":
-                area = correction(area, lorentz, zebra_mode, scan["gamma_angle"], scan["nu_angle"])
-                int_str = f'{"{:8.2f}".format(area):{align}{padding[2]}}'
-                angle_str1 = f'{scan["gamma_angle"]:{padding[3]}}'
-                angle_str2 = f'{scan["omega_angle"]:{padding[3]}}'
-                angle_str3 = f'{scan["nu_angle"]:{padding[3]}}'
-                angle_str4 = f'{scan["unkwn_angle"]:{padding[3]}}'
-
-            line = (
-                scan_number_str
-                + h_str
-                + l_str
-                + k_str
-                + int_str
-                + sigma_str
-                + angle_str1
-                + angle_str2
-                + angle_str3
-                + angle_str4
-                + "\n"
-            )
-            out_file.write(line)

pyzebra/fit2.py

@@ -59,15 +59,17 @@ def fitccl(
     constraints_min = [23, None, 50, 0, 0]
     constraints_min = [80, None, 1000, 0, 100]
     """
+    if "peak_indexes" not in scan:
+        scan["peak_indexes"] = []
+
     if len(scan["peak_indexes"]) > 1:
         # return in case of more than 1 peaks
-        print("More than 1 peak, scan skipped")
         return
+
     if binning is None or binning == 0 or binning == 1:
         x = list(scan["om"])
         y = list(scan["Counts"])
         y_err = list(np.sqrt(y)) if scan.get("sigma", None) is None else list(scan["sigma"])
-        print(scan["peak_indexes"])
         if not scan["peak_indexes"]:
             centre = np.mean(x)
         else:
@@ -87,7 +89,6 @@ def fitccl(
 
     if len(scan["peak_indexes"]) == 0:
         # Case for no peak, gaussian in centre, sigma as 20% of range
-        print("No peak")
         peak_index = find_nearest(x, np.mean(x))
         guess[0] = centre if guess[0] is None else guess[0]
         guess[1] = (x[-1] - x[0]) / 5 if guess[1] is None else guess[1]
@@ -98,7 +99,6 @@ def fitccl(
 
     elif len(scan["peak_indexes"]) == 1:
         # case for one peak, takse into account users guesses
-        print("one peak")
         peak_height = scan["peak_heights"]
         guess[0] = centre if guess[0] is None else guess[0]
         guess[1] = 0.1 if guess[1] is None else guess[1]
@@ -128,11 +128,11 @@ def fitccl(
         ("intercept", guess[4], bool(vary[4]), constraints_min[4], constraints_max[4], None, None),
     )
     # the weighted fit
+    weights = [np.abs(1 / val) if val != 0 else 1 for val in y_err]
     try:
-        result = mod.fit(
+        result = mod.fit(y, params, weights=weights, x=x, calc_covar=True)
-            y, params, weights=[np.abs(1 / val) for val in y_err], x=x, calc_covar=True,
-        )
     except ValueError:
+        print(f"Couldn't fit scan {scan['scan_number']}")
         return
 
     if result.params["g_amp"].stderr is None:
@@ -213,9 +213,9 @@ def fitccl(
     d = {}
     for pars in result.params:
         d[str(pars)] = (result.params[str(pars)].value, result.params[str(pars)].vary)
-    print(result.fit_report())
 
-    print((result.params["g_amp"].value - int_area.n) / result.params["g_amp"].value)
+    print("Scan", scan["scan_number"])
+    print(result.fit_report())
 
     d["ratio"] = (result.params["g_amp"].value - int_area.n) / result.params["g_amp"].value
     d["int_area"] = int_area
@@ -224,4 +224,5 @@ def fitccl(
     d["result"] = result
     d["comps"] = comps
     d["numfit"] = [numfit_min, numfit_max]
+    d["x_fit"] = x
     scan["fit"] = d

pyzebra/fitvol3.py

@@ -0,0 +1,167 @@
+import numpy as np
+from lmfit import Model, Parameters
+from scipy.integrate import simps
+import matplotlib.pyplot as plt
+import uncertainties as u
+from lmfit.models import GaussianModel
+from lmfit.models import VoigtModel
+from lmfit.models import PseudoVoigtModel
+
+
+def bin_data(array, binsize):
+    if isinstance(binsize, int) and 0 < binsize < len(array):
+        return [
+            np.mean(array[binsize * i : binsize * i + binsize])
+            for i in range(int(np.ceil(len(array) / binsize)))
+        ]
+    else:
+        print("Binsize need to be positive integer smaller than lenght of array")
+        return array
+
+
+def create_uncertanities(y, y_err):
+    # create array with uncertanities for error propagation
+    combined = np.array([])
+    for i in range(len(y)):
+        part = u.ufloat(y[i], y_err[i])
+        combined = np.append(combined, part)
+    return combined
+
+
+def find_nearest(array, value):
+    # find nearest value and return index
+    array = np.asarray(array)
+    idx = (np.abs(array - value)).argmin()
+    return idx
+
+
+# predefined peak positions
+# peaks = [6.2,  8.1, 9.9, 11.5]
+peaks = [23.5, 24.5]
+# peaks = [24]
+def fitccl(scan, variable="om", peak_type="gauss", binning=None):
+
+    x = list(scan[variable])
+    y = list(scan["Counts"])
+    peak_centre = np.mean(x)
+    if binning is None or binning == 0 or binning == 1:
+        x = list(scan["om"])
+        y = list(scan["Counts"])
+        y_err = list(np.sqrt(y)) if scan.get("sigma", None) is None else list(scan["sigma"])
+        print(scan["peak_indexes"])
+        if not scan["peak_indexes"]:
+            peak_centre = np.mean(x)
+        else:
+            centre = x[int(scan["peak_indexes"])]
+    else:
+        x = list(scan["om"])
+        if not scan["peak_indexes"]:
+            peak_centre = np.mean(x)
+        else:
+            peak_centre = x[int(scan["peak_indexes"])]
+        x = bin_data(x, binning)
+        y = list(scan["Counts"])
+        y_err = list(np.sqrt(y)) if scan.get("sigma", None) is None else list(scan["sigma"])
+        combined = bin_data(create_uncertanities(y, y_err), binning)
+        y = [combined[i].n for i in range(len(combined))]
+        y_err = [combined[i].s for i in range(len(combined))]
+
+    def background(x, slope, intercept):
+        """background"""
+        return slope * (x - peak_centre) + intercept
+
+    def gaussian(x, center, g_sigma, amplitude):
+        """1-d gaussian: gaussian(x, amp, cen, wid)"""
+        return (amplitude / (np.sqrt(2.0 * np.pi) * g_sigma)) * np.exp(
+            -((x - center) ** 2) / (2 * g_sigma ** 2)
+        )
+
+    def lorentzian(x, center, l_sigma, amplitude):
+        """1d lorentzian"""
+        return (amplitude / (1 + ((1 * x - center) / l_sigma) ** 2)) / (np.pi * l_sigma)
+
+    def pseudoVoigt1(x, center, g_sigma, amplitude, l_sigma, fraction):
+        """PseudoVoight peak with different widths of lorenzian and gaussian"""
+        return (1 - fraction) * gaussian(x, center, g_sigma, amplitude) + fraction * (
+            lorentzian(x, center, l_sigma, amplitude)
+        )
+
+    mod = Model(background)
+    params = Parameters()
+    params.add_many(
+        ("slope", 0, True, None, None, None, None), ("intercept", 0, False, None, None, None, None)
+    )
+    for i in range(len(peaks)):
+        if peak_type == "gauss":
+            mod = mod + GaussianModel(prefix="p%d_" % (i + 1))
+            params.add(str("p%d_" % (i + 1) + "amplitude"), 20, True, 0, None, None)
+            params.add(str("p%d_" % (i + 1) + "center"), peaks[i], True, None, None, None)
+            params.add(str("p%d_" % (i + 1) + "sigma"), 0.2, True, 0, 5, None)
+        elif peak_type == "voigt":
+            mod = mod + VoigtModel(prefix="p%d_" % (i + 1))
+            params.add(str("p%d_" % (i + 1) + "amplitude"), 20, True, 0, None, None)
+            params.add(str("p%d_" % (i + 1) + "center"), peaks[i], True, None, None, None)
+            params.add(str("p%d_" % (i + 1) + "sigma"), 0.2, True, 0, 3, None)
+            params.add(str("p%d_" % (i + 1) + "gamma"), 0.2, True, 0, 5, None)
+        elif peak_type == "pseudovoigt":
+            mod = mod + PseudoVoigtModel(prefix="p%d_" % (i + 1))
+            params.add(str("p%d_" % (i + 1) + "amplitude"), 20, True, 0, None, None)
+            params.add(str("p%d_" % (i + 1) + "center"), peaks[i], True, None, None, None)
+            params.add(str("p%d_" % (i + 1) + "sigma"), 0.2, True, 0, 5, None)
+            params.add(str("p%d_" % (i + 1) + "fraction"), 0.5, True, -5, 5, None)
+        elif peak_type == "pseudovoigt1":
+            mod = mod + Model(pseudoVoigt1, prefix="p%d_" % (i + 1))
+            params.add(str("p%d_" % (i + 1) + "amplitude"), 20, True, 0, None, None)
+            params.add(str("p%d_" % (i + 1) + "center"), peaks[i], True, None, None, None)
+            params.add(str("p%d_" % (i + 1) + "g_sigma"), 0.2, True, 0, 5, None)
+            params.add(str("p%d_" % (i + 1) + "l_sigma"), 0.2, True, 0, 5, None)
+            params.add(str("p%d_" % (i + 1) + "fraction"), 0.5, True, 0, 1, None)
+    # add parameters
+
+    result = mod.fit(
+        y, params, weights=[np.abs(1 / y_err[i]) for i in range(len(y_err))], x=x, calc_covar=True
+    )
+
+    comps = result.eval_components()
+
+    reportstring = list()
+    for keys in result.params:
+        if result.params[keys].value is not None:
+            str2 = np.around(result.params[keys].value, 3)
+        else:
+            str2 = 0
+        if result.params[keys].stderr is not None:
+            str3 = np.around(result.params[keys].stderr, 3)
+        else:
+            str3 = 0
+        reportstring.append("%s = %2.3f +/- %2.3f" % (keys, str2, str3))
+
+    reportstring = "\n".join(reportstring)
+
+    plt.figure(figsize=(20, 10))
+    plt.plot(x, result.best_fit, "k-", label="Best fit")
+
+    plt.plot(x, y, "b-", label="Original data")
+    plt.plot(x, comps["background"], "g--", label="Line component")
+    for i in range(len(peaks)):
+        plt.plot(
+            x,
+            comps[str("p%d_" % (i + 1))],
+            "r--",
+        )
+        plt.fill_between(x, comps[str("p%d_" % (i + 1))], alpha=0.4, label=str("p%d_" % (i + 1)))
+    plt.legend()
+    plt.text(
+        np.min(x),
+        np.max(y),
+        reportstring,
+        fontsize=9,
+        verticalalignment="top",
+    )
+    plt.title(str(peak_type))
+
+    plt.xlabel("Omega [deg]")
+    plt.ylabel("Counts [a.u.]")
+    plt.show()
+
+    print(result.fit_report())

pyzebra/h5.py

@@ -60,7 +60,12 @@ def read_detector_data(filepath):
         det_data["chi_angle"] = h5f["/entry1/sample/chi"][:]  # ch
         det_data["phi_angle"] = h5f["/entry1/sample/phi"][:]  # ph
         det_data["UB"] = h5f["/entry1/sample/UB"][:].reshape(3, 3)
-        det_data["magnetic_field"] = h5f["/entry1/sample/magnetic_field"][:]
+
-        det_data["temperature"] = h5f["/entry1/sample/temperature"][:]
+        # optional parameters
+        if "/entry1/sample/magnetic_field" in h5f:
+            det_data["magnetic_field"] = h5f["/entry1/sample/magnetic_field"][:]
+
+        if "/entry1/sample/temperature" in h5f:
+            det_data["temperature"] = h5f["/entry1/sample/temperature"][:]
 
     return det_data

pyzebra/param_study_moduls.py

@@ -1,12 +1,24 @@
-from load_1D import load_1D
-from ccl_dict_operation import add_dict
-import pandas as pd
-from mpl_toolkits.mplot3d import Axes3D  # dont delete, otherwise waterfall wont work
-import matplotlib.pyplot as plt
-import matplotlib as mpl
-import numpy as np
 import pickle
+
+import matplotlib as mpl
+import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
 import scipy.io as sio
+import uncertainties as u
+from mpl_toolkits.mplot3d import Axes3D  # dont delete, otherwise waterfall wont work
+import collections
+
+from .ccl_io import load_1D
+
+def create_tuples(x, y, y_err):
+    """creates tuples for sorting and merginng of the data
+    Counts need to be normalized to monitor before"""
+    t = list()
+    for i in range(len(x)):
+        tup = (x[i], y[i], y_err[i])
+        t.append(tup)
+    return t
 
 
 def load_dats(filepath):
@@ -37,45 +49,45 @@ def load_dats(filepath):
             if data_type == "txt":
                 dict1 = add_dict(dict1, load_1D(file_list[i][0]))
             else:
+
                 dict1 = add_dict(dict1, load_1D(file_list[i]))
         dict1["scan"][i + 1]["params"] = {}
         if data_type == "txt":
             for x in range(len(col_names) - 1):
-                dict1["scan"][i + 1]["params"][col_names[x + 1]] = file_list[i][x + 1]
+                dict1["scan"][i + 1]["params"][col_names[x + 1]] = float(file_list[i][x + 1])
-
     return dict1
 
 
-def create_dataframe(dict1):
+def create_dataframe(dict1, variables):
     """Creates pandas dataframe from the dictionary
     :arg ccl like dictionary
     :return pandas dataframe"""
     # create dictionary to which we pull only wanted items before transforming it to pd.dataframe
     pull_dict = {}
     pull_dict["filenames"] = list()
-    for key in dict1["scan"][1]["params"]:
+    for keys in variables:
-        pull_dict[key] = list()
+        for item in variables[keys]:
-    pull_dict["temperature"] = list()
+            pull_dict[item] = list()
-    pull_dict["mag_field"] = list()
     pull_dict["fit_area"] = list()
     pull_dict["int_area"] = list()
-    pull_dict["om"] = list()
     pull_dict["Counts"] = list()
 
+    for keys in pull_dict:
+        print(keys)
+
     # populate the dict
     for keys in dict1["scan"]:
         if "file_of_origin" in dict1["scan"][keys]:
             pull_dict["filenames"].append(dict1["scan"][keys]["file_of_origin"].split("/")[-1])
         else:
             pull_dict["filenames"].append(dict1["meta"]["original_filename"].split("/")[-1])
-        for key in dict1["scan"][keys]["params"]:
+
-            pull_dict[str(key)].append(float(dict1["scan"][keys]["params"][key]))
-        pull_dict["temperature"].append(dict1["scan"][keys]["temperature"])
-        pull_dict["mag_field"].append(dict1["scan"][keys]["mag_field"])
         pull_dict["fit_area"].append(dict1["scan"][keys]["fit"]["fit_area"])
         pull_dict["int_area"].append(dict1["scan"][keys]["fit"]["int_area"])
-        pull_dict["om"].append(dict1["scan"][keys]["om"])
         pull_dict["Counts"].append(dict1["scan"][keys]["Counts"])
+        for key in variables:
+            for i in variables[key]:
+                pull_dict[i].append(_finditem(dict1["scan"][keys], i))
 
     return pd.DataFrame(data=pull_dict)
 
@@ -144,7 +156,7 @@ def make_graph(data, sorting_parameter, style):
 
 
 def save_dict(obj, name):
-    """ saves dictionary as pickle file in binary format
+    """saves dictionary as pickle file in binary format
     :arg obj - object to save
     :arg name - name of the file
     NOTE: path should be added later"""
@@ -200,3 +212,277 @@ def save_table(data, filetype, name, path=None):
         hdf.close()
     if filetype == "json":
         data.to_json((path + name + ".json"))
+
+
+def normalize(scan, monitor):
+    """Normalizes the measurement to monitor, checks if sigma exists, otherwise creates it
+    :arg dict : dictionary to from which to tkae the scan
+    :arg key : which scan to normalize from dict1
+    :arg monitor : final monitor
+    :return counts - normalized counts
+    :return sigma - normalized sigma"""
+
+    counts = np.array(scan["Counts"])
+    sigma = np.sqrt(counts) if "sigma" not in scan else scan["sigma"]
+    monitor_ratio = monitor / scan["monitor"]
+    scaled_counts = counts * monitor_ratio
+    scaled_sigma = np.array(sigma) * monitor_ratio
+
+    return scaled_counts, scaled_sigma
+
+
+def merge(scan1, scan2, keep=True, monitor=100000):
+    """merges the two tuples and sorts them, if om value is same, Counts value is average
+    averaging is propagated into sigma if dict1 == dict2, key[1] is deleted after merging
+    :arg dict1 : dictionary to which measurement will be merged
+    :arg dict2 : dictionary from which measurement will be merged
+    :arg scand_dict_result : result of scan_dict after auto function
+    :arg keep : if true, when monitors are same, does not change it, if flase, takes monitor
+    always
+    :arg monitor : final monitor after merging
+    note: dict1 and dict2 can be same dict
+    :return dict1 with merged scan"""
+
+    if keep:
+        if scan1["monitor"] == scan2["monitor"]:
+            monitor = scan1["monitor"]
+
+    # load om and Counts
+    x1, x2 = scan1["om"], scan2["om"]
+    cor_y1, y_err1 = normalize(scan1, monitor=monitor)
+    cor_y2, y_err2 = normalize(scan2, monitor=monitor)
+    # creates touples (om, Counts, sigma) for sorting and further processing
+    tuple_list = create_tuples(x1, cor_y1, y_err1) + create_tuples(x2, cor_y2, y_err2)
+    # Sort the list on om and add 0 0 0 tuple to the last position
+    sorted_t = sorted(tuple_list, key=lambda tup: tup[0])
+    sorted_t.append((0, 0, 0))
+    om, Counts, sigma = [], [], []
+    seen = list()
+    for i in range(len(sorted_t) - 1):
+        if sorted_t[i][0] not in seen:
+            if sorted_t[i][0] != sorted_t[i + 1][0]:
+                om = np.append(om, sorted_t[i][0])
+                Counts = np.append(Counts, sorted_t[i][1])
+                sigma = np.append(sigma, sorted_t[i][2])
+            else:
+                om = np.append(om, sorted_t[i][0])
+                counts1, counts2 = sorted_t[i][1], sorted_t[i + 1][1]
+                sigma1, sigma2 = sorted_t[i][2], sorted_t[i + 1][2]
+                count_err1 = u.ufloat(counts1, sigma1)
+                count_err2 = u.ufloat(counts2, sigma2)
+                avg = (count_err1 + count_err2) / 2
+                Counts = np.append(Counts, avg.n)
+                sigma = np.append(sigma, avg.s)
+                seen.append(sorted_t[i][0])
+        else:
+            continue
+    scan1["om"] = om
+    scan1["Counts"] = Counts
+    scan1["sigma"] = sigma
+    scan1["monitor"] = monitor
+    print("merging done")
+
+
+def add_dict(dict1, dict2):
+    """adds two dictionaries, meta of the new is saved as meata+original_filename and
+    measurements are shifted to continue with numbering of first dict
+    :arg dict1 : dictionarry to add to
+    :arg dict2 : dictionarry from which to take the measurements
+    :return dict1 : combined dictionary
+    Note: dict1 must be made from ccl, otherwise we would have to change the structure of loaded
+    dat file"""
+    try:
+        if dict1["meta"]["zebra_mode"] != dict2["meta"]["zebra_mode"]:
+            print("You are trying to add scans measured with different zebra modes")
+            return
+    # this is for the qscan case
+    except KeyError:
+        print("Zebra mode not specified")
+    max_measurement_dict1 = max([keys for keys in dict1["scan"]])
+    new_filenames = np.arange(
+        max_measurement_dict1 + 1, max_measurement_dict1 + 1 + len(dict2["scan"])
+    )
+    new_meta_name = "meta" + str(dict2["meta"]["original_filename"])
+    if new_meta_name not in dict1:
+        for keys, name in zip(dict2["scan"], new_filenames):
+            dict2["scan"][keys]["file_of_origin"] = str(dict2["meta"]["original_filename"])
+            dict1["scan"][name] = dict2["scan"][keys]
+
+        dict1[new_meta_name] = dict2["meta"]
+    else:
+        raise KeyError(
+            str(
+                "The file %s has alredy been added to %s"
+                % (dict2["meta"]["original_filename"], dict1["meta"]["original_filename"])
+            )
+        )
+    return dict1
+
+
+def auto(dict):
+    """takes just unique tuples from all tuples in dictionary returend by scan_dict
+    intendet for automatic merge if you doesent want to specify what scans to merge together
+    args: dict - dictionary from scan_dict function
+    :return dict - dict without repetitions"""
+    for keys in dict:
+        tuple_list = dict[keys]
+        new = list()
+        for i in range(len(tuple_list)):
+            if tuple_list[0][0] == tuple_list[i][0]:
+                new.append(tuple_list[i])
+        dict[keys] = new
+    return dict
+
+
+def scan_dict(dict, precision=0.5):
+    """scans dictionary for duplicate angles indexes
+    :arg dict : dictionary to scan
+    :arg precision : in deg, sometimes angles are zero so its easier this way, instead of
+    checking zero division
+    :return  dictionary with matching scans, if there are none, the dict is empty
+    note: can be checked by "not d", true if empty
+    """
+
+    if dict["meta"]["zebra_mode"] == "bi":
+        angles = ["twotheta_angle", "omega_angle", "chi_angle", "phi_angle"]
+    elif dict["meta"]["zebra_mode"] == "nb":
+        angles = ["gamma_angle", "omega_angle", "nu_angle"]
+    else:
+        print("Unknown zebra mode")
+        return
+
+    d = {}
+    for i in dict["scan"]:
+        for j in dict["scan"]:
+            if dict["scan"][i] != dict["scan"][j]:
+                itup = list()
+                for k in angles:
+                    itup.append(abs(abs(dict["scan"][i][k]) - abs(dict["scan"][j][k])))
+
+                if all(i <= precision for i in itup):
+                    print(itup)
+                    print([dict["scan"][i][k] for k in angles])
+                    print([dict["scan"][j][k] for k in angles])
+                    if str([np.around(dict["scan"][i][k], 0) for k in angles]) not in d:
+                        d[str([np.around(dict["scan"][i][k], 0) for k in angles])] = list()
+                        d[str([np.around(dict["scan"][i][k], 0) for k in angles])].append((i, j))
+                    else:
+                        d[str([np.around(dict["scan"][i][k], 0) for k in angles])].append((i, j))
+
+                else:
+                    pass
+
+            else:
+                continue
+
+    return d
+
+
+def _finditem(obj, key):
+    if key in obj:
+        return obj[key]
+    for k, v in obj.items():
+        if isinstance(v, dict):
+            item = _finditem(v, key)
+            if item is not None:
+                return item
+
+
+def most_common(lst):
+    return max(set(lst), key=lst.count)
+
+
+def variables(dictionary):
+    """Funcrion to guess what variables will be used in the param study
+    i call pripary variable the one the array like variable, usually omega
+    and secondary the slicing variable, different for each scan,for example temperature"""
+    # find all variables that are in all scans
+    stdev_precision = 0.05
+    all_vars = list()
+    for keys in dictionary["scan"]:
+        all_vars.append([key for key in dictionary["scan"][keys] if key != "params"])
+        if dictionary["scan"][keys]["params"]:
+            all_vars.append(key for key in dictionary["scan"][keys]["params"])
+
+    all_vars = [i for sublist in all_vars for i in sublist]
+    # get the ones that are in all scans
+    b = collections.Counter(all_vars)
+    inall = [key for key in b if b[key] == len(dictionary["scan"])]
+    # delete those that are obviously wrong
+    wrong = [
+        "NP",
+        "Counts",
+        "Monitor1",
+        "Monitor2",
+        "Monitor3",
+        "h_index",
+        "l_index",
+        "k_index",
+        "n_points",
+        "monitor",
+        "Time",
+        "omega_angle",
+        "twotheta_angle",
+        "chi_angle",
+        "phi_angle",
+        "nu_angle",
+    ]
+    inall_red = [i for i in inall if i not in wrong]
+
+    # check for primary variable, needs to be list, we dont suspect the
+    # primary variable be as a parameter (be in scan[params])
+    primary_candidates = list()
+    for key in dictionary["scan"]:
+        for i in inall_red:
+            if isinstance(_finditem(dictionary["scan"][key], i), list):
+                if np.std(_finditem(dictionary["scan"][key], i)) > stdev_precision:
+                    primary_candidates.append(i)
+    # check which of the primary are in every scan
+    primary_candidates = collections.Counter(primary_candidates)
+    second_round_primary_candidates = [
+        key for key in primary_candidates if primary_candidates[key] == len(dictionary["scan"])
+    ]
+
+    if len(second_round_primary_candidates) == 1:
+        print("We've got a primary winner!", second_round_primary_candidates)
+    else:
+        print("Still not sure with primary:(", second_round_primary_candidates)
+
+    # check for secondary variable, we suspect a float\int or not changing array
+    # we dont need to check for primary ones
+    secondary_candidates = [i for i in inall_red if i not in second_round_primary_candidates]
+    # print("secondary candidates", secondary_candidates)
+    # select arrays and floats and ints
+    second_round_secondary_candidates = list()
+    for key in dictionary["scan"]:
+        for i in secondary_candidates:
+            if isinstance(_finditem(dictionary["scan"][key], i), float):
+                second_round_secondary_candidates.append(i)
+            elif isinstance(_finditem(dictionary["scan"][key], i), int):
+                second_round_secondary_candidates.append(i)
+            elif isinstance(_finditem(dictionary["scan"][key], i), list):
+                if np.std(_finditem(dictionary["scan"][key], i)) < stdev_precision:
+                    second_round_secondary_candidates.append(i)
+
+    second_round_secondary_candidates = collections.Counter(second_round_secondary_candidates)
+    second_round_secondary_candidates = [
+        key
+        for key in second_round_secondary_candidates
+        if second_round_secondary_candidates[key] == len(dictionary["scan"])
+    ]
+    # print("secondary candidates after second round", second_round_secondary_candidates)
+    # now we check if they vary between the scans
+    third_round_sec_candidates = list()
+    for i in second_round_secondary_candidates:
+        check_array = list()
+        for keys in dictionary["scan"]:
+            check_array.append(np.average(_finditem(dictionary["scan"][keys], i)))
+        # print(i, check_array, np.std(check_array))
+        if np.std(check_array) > stdev_precision:
+            third_round_sec_candidates.append(i)
+    if len(third_round_sec_candidates) == 1:
+        print("We've got a secondary winner!", third_round_sec_candidates)
+    else:
+        print("Still not sure with secondary :(", third_round_sec_candidates)
+
+    return {"primary": second_round_primary_candidates, "secondary": third_round_sec_candidates}