Updating for version 0.6.5

Fix #47

pyzebra/__init__.py

@@ -5,4 +5,4 @@ from pyzebra.h5 import *
 from pyzebra.utils import *
 from pyzebra.xtal import *
 
-__version__ = "0.6.1"
+__version__ = "0.6.5"

pyzebra/app/panel_ccl_compare.py

@@ -178,7 +178,7 @@ def create():
 
         new_data1 = []
         new_data2 = []
-        for ind, f_str, f_name in enumerate(zip(upload_button.value, upload_button.filename)):
+        for ind, (f_str, f_name) in enumerate(zip(upload_button.value, upload_button.filename)):
             with io.StringIO(base64.b64decode(f_str).decode()) as file:
                 base, ext = os.path.splitext(f_name)
                 try:

pyzebra/app/panel_hdf_param_study.py

@@ -141,22 +141,29 @@ def create():
 
         scan_table_source.data.update(frame=frame, x_pos=x_pos, y_pos=y_pos)
 
+    def _file_open():
+        new_data = []
+        for f_name in file_select.value:
+            try:
+                new_data.append(pyzebra.read_detector_data(f_name))
+            except KeyError:
+                print("Could not read data from the file.")
+                return
+
+        zebra_data.extend(new_data)
+
+        _init_datatable()
+
     def file_open_button_callback():
         nonlocal zebra_data
         zebra_data = []
-        for f_name in file_select.value:
-            zebra_data.append(pyzebra.read_detector_data(f_name))
-
-        _init_datatable()
+        _file_open()
 
     file_open_button = Button(label="Open New", width=100)
     file_open_button.on_click(file_open_button_callback)
 
     def file_append_button_callback():
-        for f_name in file_select.value:
-            zebra_data.append(pyzebra.read_detector_data(f_name))
-
-        _init_datatable()
+        _file_open()
 
     file_append_button = Button(label="Append", width=100)
     file_append_button.on_click(file_append_button_callback)

pyzebra/app/panel_hdf_viewer.py

@@ -107,13 +107,23 @@ def create():
     upload_cami_button = FileInput(accept=".cami", width=200)
     upload_cami_button.on_change("value", upload_cami_button_callback)
 
-    def _open_file(file, cami_meta):
+    def _file_open(file, cami_meta):
         nonlocal det_data
-        det_data = pyzebra.read_detector_data(file, cami_meta)
+        try:
+            det_data = pyzebra.read_detector_data(file, cami_meta)
+        except KeyError:
+            print("Could not read data from the file.")
+            return
+
+        last_im_index = det_data["data"].shape[0] - 1
 
         index_spinner.value = 0
-        index_spinner.high = det_data["data"].shape[0] - 1
-        index_slider.end = det_data["data"].shape[0] - 1
+        index_spinner.high = last_im_index
+        if last_im_index == 0:
+            index_slider.disabled = True
+        else:
+            index_slider.disabled = False
+            index_slider.end = last_im_index
 
         zebra_mode = det_data["zebra_mode"]
         if zebra_mode == "nb":
@@ -125,7 +135,7 @@ def create():
         update_overview_plot()
 
     def upload_hdf_button_callback(_attr, _old, new):
-        _open_file(io.BytesIO(base64.b64decode(new)), None)
+        _file_open(io.BytesIO(base64.b64decode(new)), None)
 
     upload_hdf_div = Div(text="or upload .hdf file:", margin=(5, 5, 0, 5))
     upload_hdf_button = FileInput(accept=".hdf", width=200)
@@ -136,9 +146,9 @@ def create():
             return
 
         if data_source.value == "proposal number":
-            _open_file(file_select.value[0], None)
+            _file_open(file_select.value[0], None)
         else:
-            _open_file(file_select.value[0], cami_meta)
+            _file_open(file_select.value[0], cami_meta)
 
     file_open_button = Button(label="Open New", width=100)
     file_open_button.on_click(file_open_button_callback)
@@ -249,7 +259,7 @@ def create():
 
         var = det_data[scan_motor]
         var_start = var[0]
-        var_end = var[-1] + (var[-1] - var[0]) / (n_im - 1)
+        var_end = var[-1] + (var[-1] - var[0]) / (n_im - 1) if n_im != 1 else var_start + 1
 
         scanning_motor_range.start = var_start
         scanning_motor_range.end = var_end

pyzebra/app/panel_param_study.py

@@ -27,6 +27,7 @@ from bokeh.models import (
     Legend,
     Line,
     LinearAxis,
+    LinearColorMapper,
     MultiLine,
     MultiSelect,
     NumberEditor,
@@ -34,6 +35,7 @@ from bokeh.models import (
     PanTool,
     Plot,
     RadioGroup,
+    Range1d,
     ResetTool,
     Scatter,
     Select,
@@ -46,8 +48,7 @@ from bokeh.models import (
     WheelZoomTool,
     Whisker,
 )
-from bokeh.palettes import Category10, Turbo256
-from bokeh.transform import linear_cmap
+from bokeh.palettes import Category10, Plasma256
 from scipy import interpolate
 
 import pyzebra
@@ -337,24 +338,31 @@ def create():
 
         ov_plot_mline_source.data.update(xs=xs, ys=ys, param=param, color=color_palette(len(xs)))
 
-        if y:
-            mapper["transform"].low = np.min([np.min(y) for y in ys])
-            mapper["transform"].high = np.max([np.max(y) for y in ys])
-        ov_param_plot_scatter_source.data.update(x=x, y=y, param=par)
+        ov_param_plot_scatter_source.data.update(x=x, y=y)
 
-        try:
-            interp_f = interpolate.interp2d(x, y, par)
+        if y:
             x1, x2 = min(x), max(x)
             y1, y2 = min(y), max(y)
-            image = interp_f(
-                np.linspace(x1, x2, ov_param_plot.inner_width // 10),
-                np.linspace(y1, y2, ov_param_plot.inner_height // 10),
-                assume_sorted=True,
+            grid_x, grid_y = np.meshgrid(
+                np.linspace(x1, x2, ov_param_plot.inner_width),
+                np.linspace(y1, y2, ov_param_plot.inner_height),
             )
+            image = interpolate.griddata((x, y), par, (grid_x, grid_y))
             ov_param_plot_image_source.data.update(
                 image=[image], x=[x1], y=[y1], dw=[x2 - x1], dh=[y2 - y1]
             )
-        except Exception:
+
+            x_range = ov_param_plot.x_range
+            x_range.start, x_range.end = x1, x2
+            x_range.reset_start, x_range.reset_end = x1, x2
+            x_range.bounds = (x1, x2)
+
+            y_range = ov_param_plot.y_range
+            y_range.start, y_range.end = y1, y2
+            y_range.reset_start, y_range.reset_end = y1, y2
+            y_range.bounds = (y1, y2)
+
+        else:
             ov_param_plot_image_source.data.update(image=[], x=[], y=[], dw=[], dh=[])
 
     def _update_param_plot():
@@ -448,9 +456,7 @@ def create():
     ov_plot.toolbar.logo = None
 
     # Overview perams plot
-    ov_param_plot = Plot(
-        x_range=DataRange1d(), y_range=DataRange1d(), plot_height=450, plot_width=700
-    )
+    ov_param_plot = Plot(x_range=Range1d(), y_range=Range1d(), plot_height=450, plot_width=700)
 
     ov_param_plot.add_layout(LinearAxis(axis_label="Param"), place="left")
     ov_param_plot.add_layout(LinearAxis(axis_label="Scan motor"), place="below")
@@ -458,16 +464,16 @@ def create():
     ov_param_plot.add_layout(Grid(dimension=0, ticker=BasicTicker()))
     ov_param_plot.add_layout(Grid(dimension=1, ticker=BasicTicker()))
 
+    color_mapper = LinearColorMapper(palette=Plasma256)
     ov_param_plot_image_source = ColumnDataSource(dict(image=[], x=[], y=[], dw=[], dh=[]))
     ov_param_plot.add_glyph(
-        ov_param_plot_image_source, Image(image="image", x="x", y="y", dw="dw", dh="dh")
+        ov_param_plot_image_source,
+        Image(image="image", x="x", y="y", dw="dw", dh="dh", color_mapper=color_mapper),
     )
 
-    ov_param_plot_scatter_source = ColumnDataSource(dict(x=[], y=[], param=[]))
-    mapper = linear_cmap(field_name="param", palette=Turbo256, low=0, high=50)
+    ov_param_plot_scatter_source = ColumnDataSource(dict(x=[], y=[]))
     ov_param_plot.add_glyph(
-        ov_param_plot_scatter_source,
-        Scatter(x="x", y="y", line_color=mapper, fill_color=mapper, size=10),
+        ov_param_plot_scatter_source, Scatter(x="x", y="y", marker="dot", size=15),
     )
 
     ov_param_plot.add_tools(PanTool(), WheelZoomTool(), ResetTool())

pyzebra/ccl_io.py

@@ -170,7 +170,7 @@ def parse_1D(fileobj, data_type):
             while len(counts) < s["n_points"]:
                 counts.extend(map(float, next(fileobj).split()))
             s["counts"] = np.array(counts)
-            s["counts_err"] = np.sqrt(s["counts"])
+            s["counts_err"] = np.sqrt(np.maximum(s["counts"], 1))
 
             if s["h"].is_integer() and s["k"].is_integer() and s["l"].is_integer():
                 s["h"], s["k"], s["l"] = map(int, (s["h"], s["k"], s["l"]))
@@ -208,7 +208,7 @@ def parse_1D(fileobj, data_type):
         for name in col_names:
             s[name] = np.array(s[name])
 
-        s["counts_err"] = np.sqrt(s["counts"])
+        s["counts_err"] = np.sqrt(np.maximum(s["counts"], 1))
 
         s["scan_motors"] = []
         for motor, step in zip(motors, steps):

pyzebra/ccl_process.py

@@ -131,7 +131,7 @@ def merge_scans(scan_into, scan_from):
 
     scan_into[scan_motor] = pos_tmp
     scan_into["counts"] = val_tmp / num_tmp
-    scan_into["counts_err"] = np.sqrt(err_tmp)
+    scan_into["counts_err"] = np.sqrt(err_tmp) / num_tmp
 
     scan_from["export"] = False
 
@@ -220,8 +220,7 @@ def fit_scan(scan, model_dict, fit_from=None, fit_to=None):
         else:
             model += _model
 
-    weights = [1 / y_err if y_err != 0 else 1 for y_err in y_err]
-    scan["fit"] = model.fit(y_fit, x=x_fit, weights=weights)
+    scan["fit"] = model.fit(y_fit, x=x_fit, weights=1 / y_err)
 
 
 def get_area(scan, area_method, lorentz):

pyzebra/h5.py

@@ -103,12 +103,16 @@ def read_detector_data(filepath, cami_meta=None):
         det_data["name"] = h5f["/entry1/sample/name"][0].decode()
         det_data["cell"] = h5f["/entry1/sample/cell"][:]
 
-        for var in ("omega", "gamma", "nu", "chi", "phi"):
-            if abs(det_data[var][0] - det_data[var][-1]) > 0.1:
-                det_data["scan_motor"] = var
-                break
+        if n == 1:
+            # a default motor for a single frame file
+            det_data["scan_motor"] = "omega"
         else:
-            raise ValueError("No angles that vary")
+            for var in ("omega", "gamma", "nu", "chi", "phi"):
+                if abs(det_data[var][0] - det_data[var][-1]) > 0.1:
+                    det_data["scan_motor"] = var
+                    break
+            else:
+                raise ValueError("No angles that vary")
 
         # optional parameters
         if "/entry1/sample/magnetic_field" in h5f:
@@ -132,7 +136,7 @@ def read_detector_data(filepath, cami_meta=None):
 
             if "detector parameters" in cami_meta:
                 cami_meta_detparam = cami_meta["detector parameters"]
-                if "dist1" in cami_meta_detparam:
-                    det_data["ddist"] = cami_meta_detparam["dist1"]
+                if "dist2" in cami_meta_detparam:
+                    det_data["ddist"] = cami_meta_detparam["dist2"]
 
     return det_data