Add initial implementation of io funcs and webapp

pyzebra/__init__.py

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+from pyzebra.zebra import *

pyzebra/app.py

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+import numpy as np
+from bokeh.io import curdoc
+from bokeh.layouts import column, row
+from bokeh.models import (
+    BasicTicker,
+    Button,
+    ColumnDataSource,
+    Range1d,
+    Grid,
+    HoverTool,
+    Image,
+    LinearAxis,
+    PanTool,
+    Plot,
+    ResetTool,
+    SaveTool,
+    WheelZoomTool,
+    Dropdown,
+    TextInput,
+    Toggle,
+    Spinner,
+)
+
+import pyzebra
+
+
+IMAGE_W = 256
+IMAGE_H = 128
+
+doc = curdoc()
+
+global curent_h5_data, current_index
+
+
+def update_image():
+    image_source.data.update(image=[curent_h5_data[current_index]])
+    index_spinner.value = current_index
+
+
+def filelist_callback(_attr, _old, new):
+    global curent_h5_data, current_index
+    data = pyzebra.read_detector_data(new)
+    curent_h5_data = data
+    current_index = 0
+    update_image()
+
+
+filelist = Dropdown()
+filelist.on_change("value", filelist_callback)
+
+
+def fileinput_callback(_attr, _old, new):
+    cami_list = pyzebra.read_cami(new)
+    file_list = cami_list["filelist"]
+    filelist.menu = file_list
+
+
+fileinput = TextInput()
+fileinput.on_change("value", fileinput_callback)
+#fileinput.value = "/home/usov_i/psi-projects/sinq/data/1.cami"
+
+
+def index_spinner_callback(_attr, _old, new):
+    global current_index
+    if 0 <= new < curent_h5_data.shape[0]:
+        current_index = new
+        update_image()
+
+
+index_spinner = Spinner(value=0)
+index_spinner.on_change("value", index_spinner_callback)
+
+plot = Plot(
+    x_range=Range1d(0, IMAGE_W, bounds=(0, IMAGE_W)),
+    y_range=Range1d(0, IMAGE_H, bounds=(0, IMAGE_H)),
+    plot_height=IMAGE_H * 3,
+    plot_width=IMAGE_W * 3,
+    toolbar_location="left",
+)
+
+# ---- tools
+plot.toolbar.logo = None
+
+hovertool = HoverTool(tooltips=[("intensity", "@image")], names=["image_glyph"])
+
+plot.add_tools(PanTool(), WheelZoomTool(maintain_focus=False), SaveTool(), ResetTool(), hovertool)
+plot.toolbar.active_scroll = plot.tools[1]
+
+# ---- axes
+plot.add_layout(LinearAxis(), place="above")
+plot.add_layout(LinearAxis(major_label_orientation="vertical"), place="right")
+
+# ---- grid lines
+plot.add_layout(Grid(dimension=0, ticker=BasicTicker()))
+plot.add_layout(Grid(dimension=1, ticker=BasicTicker()))
+
+# ---- rgba image glyph
+image_source = ColumnDataSource(
+    dict(image=[np.zeros((1, 1), dtype="float32")], x=[0], y=[0], dw=[IMAGE_W], dh=[IMAGE_H],)
+)
+
+image_glyph = Image(image="image", x="x", y="y", dw="dw", dh="dh")
+image_renderer = plot.add_glyph(image_source, image_glyph, name="image_glyph")
+
+
+def prev_button_callback():
+    global current_index
+    if current_index > 0:
+        current_index -= 1
+    update_image()
+
+
+prev_button = Button(label="Previous")
+prev_button.on_click(prev_button_callback)
+
+
+def next_button_callback():
+    global current_index
+    if current_index < curent_h5_data.shape[0] - 1:
+        current_index += 1
+    update_image()
+
+
+next_button = Button(label="Next")
+next_button.on_click(next_button_callback)
+
+
+def animate():
+    next_button_callback()
+
+
+def animate_toggle_callback(active):
+    global cb
+    if active:
+        cb = doc.add_periodic_callback(animate, 300)
+    else:
+        doc.remove_periodic_callback(cb)
+
+
+animate_toggle = Toggle(label="Animate")
+animate_toggle.on_click(animate_toggle_callback)
+
+doc.add_root(
+    column(
+        fileinput, filelist, plot, row(prev_button, next_button), row(index_spinner, animate_toggle)
+    )
+)

pyzebra/zebra.py

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+import h5py
+
+
+def read_cami(filepath):
+    """Read and parse content of a cami file.
+
+    Args:
+        filepath (str): File path of a cami file.
+
+    Returns:
+        dict: A dictionary with section names and their content.
+    """
+    cami_content = dict()
+    with open(filepath, "r") as cami_file:
+        line = cami_file.readline()
+        while line:
+            if line.startswith("#begin"):
+                # read section
+                section = line[7:-1]  # len("#begin ") = 7
+                cami_content[section] = []
+                line = cami_file.readline()
+                while not line.startswith("#end"):
+                    cami_content[section].append(line[:-1])
+                    line = cami_file.readline()
+
+            # read next line after section's end
+            line = cami_file.readline()
+
+    return cami_content
+
+
+def read_detector_data(filepath):
+    """Read detector data from an h5 file.
+
+    Args:
+        filepath (str): File path of an h5 file.
+
+    Returns:
+        ndarray: A 3D array of data.
+    """
+    with h5py.File(filepath, "r") as h5f:
+        detector_data = h5f["/entry1/area_detector2/data"][:]
+
+        # reshape data to a correct shape (2006 issue)
+        n, cols, rows = detector_data.shape
+        detector_data = detector_data.reshape(n, rows, cols)
+
+    return detector_data
+
+
+def open_cami(filepath):
+    """Open cami scan (?)
+
+    Args:
+        filepath (str): File path of a cami file.
+
+    Returns:
+        dict: A dictionary with h5 names and their detector data.
+    """
+    data = dict()
+    cami_content = read_cami(filepath)
+    for file in cami_content["filelist"]:
+        data[file] = read_detector_data(file)
+
+    return data