Added reader for SST files and hover tool

glue_solar/__init__.py

@@ -11,4 +11,6 @@
 def setup():
     from glue.viewers.image.qt import ImageViewer
     from glue_solar.pixel_extraction import PixelExtractionTool  # noqa
+    from glue_solar.pixel_hover import HoverExtractionTool
     ImageViewer.tools.append('solar:pixel_extraction')
+    ImageViewer.tools.append('solar:hover_extraction')

glue_solar/instruments/__init__.py

@@ -1 +1,2 @@
 from .iris import _parse_iris_raster
+from .sst import read_lapalma

glue_solar/instruments/sst.py

@@ -0,0 +1,120 @@
+"""
+A reader for 'La Palma' datacubes from the Swedish 1-m Solar Telescope
+"""
+import numpy as np
+from glue.config import data_factory
+from glue.core.data_factories import has_extension
+from glue.core import Data
+
+
+def lp_getheader(filename):
+    """
+    Reads header from La Palma format cube.
+
+    Parameters
+    ----------
+    filename : str
+        File to read header from.
+
+    Returns
+    -------
+    result : list
+        List with shape tuple (nx, ny [, nt]),
+        datatype (with endianness), header string.
+    """
+    # read header and convert to string
+    h = np.fromfile(filename, dtype='uint8', count=512)
+    header = ''
+    for s in h[h > 0]:
+        header += chr(s)
+    # start reading at 'datatype'
+    hd = header[header.lower().find('datatype'):]
+    hd = hd.split(':')[0].replace(',', ' ').split()
+    # Types:   uint8  int16 int32 float32
+    typelist = ['u1', 'i2', 'i4', 'f4']
+    # extract datatype
+    try:
+        dtype = typelist[int(hd[0].split('=')[1]) - 1]
+    except:
+        print(header)
+        raise IOError('lp_getheader: datatype invalid or missing')
+    # extract endianness
+    try:
+        if hd[-1].split('=')[0].lower() != 'endian':
+            raise IndexError()
+        endian = hd[-1].split('=')[1]
+    except IndexError:
+        print(header)
+        raise IOError('lp_getheader: endianess missing.')
+    if endian.lower() == 'l':
+        dtype = '<' + dtype
+    else:
+        dtype = '>' + dtype
+    # extract dims
+    try:
+        if hd[2].split('=')[0].lower() != 'dims':
+            raise IndexError()
+        dims = int(hd[2].split('=')[1])
+        if dims not in [2, 3]:
+            raise ValueError('Invalid dims=%i (must be 2 or 3)' % dims)
+    except IndexError:
+        print(header)
+        raise IOError('lp_getheader: dims invalid or missing.')
+    try:
+        if hd[3].split('=')[0].lower() != 'nx':
+            raise IndexError()
+        nx = int(hd[3].split('=')[1])
+    except:
+        print(header)
+        raise IOError('lp_getheader: nx invalid or missing.')
+    try:
+        if hd[4].split('=')[0].lower() != 'ny':
+            raise IndexError()
+        ny = int(hd[4].split('=')[1])
+    except:
+        print(header)
+        raise IOError('lp_getheader: ny invalid or missing.')
+    if dims == 3:
+        try:
+            if hd[5].split('=')[0].lower() != 'nt':
+                raise IndexError()
+            nt = int(hd[5].split('=')[1])
+        except:
+            print(header)
+            raise IOError('lp_getheader: nt invalid or missing.')
+        shape = (nx, ny, nt)
+    else:
+        shape = (nx, ny)
+    return [shape, dtype, header]
+
+
+def lp_getdata(filename, rw=False, verbose=False):
+    """
+    Reads La Palma format cube into a memmap object.
+
+    Parameters
+    ----------
+    filename : str
+        File to read.
+    rw : bool, optional
+        If True, then any change to the data will be written to file.
+    verbose : bool, optional
+        If True, will print out additional information.
+
+    Returns
+    -------
+    data : ndarray
+        Numpy memmap object with data.
+    """
+    sh, dt, header = lp_getheader(filename)
+    if verbose:
+        print(('Reading %s...\n%s' % (filename, header)))
+    mode = ['c', 'r+']
+    return np.memmap(filename, mode=mode[rw], shape=sh, dtype=dt, order='F',
+                     offset=512)
+
+
+@data_factory('La Palma cube', has_extension('fcube icube'), default='fcube icube')
+def read_lapalma(file_name):
+    data = lp_getdata(file_name)
+    return Data(cube=data)

glue_solar/pixel_hover.py

@@ -0,0 +1,75 @@
+from __future__ import absolute_import, division, print_function
+
+from glue.config import viewer_tool
+
+from glue.core.data_derived import IndexedData
+
+from glue.viewers.matplotlib.toolbar_mode import ToolbarModeBase
+
+__all__ = ['HoverExtractionTool']
+
+
+@viewer_tool
+class HoverExtractionTool(ToolbarModeBase):
+    """
+    Create a derived dataset corresponding to the selected pixel.
+    """
+
+    icon = "glue_cross"
+    tool_id = 'solar:hover_extraction'
+    action_text = 'Pixel'
+    tool_tip = 'Show data for a single pixel based on mouse location'
+    status_tip = 'Mouse over to update the extracted dataset in real time'
+
+    _pressed = False
+
+    def __init__(self, *args, **kwargs):
+        super(HoverExtractionTool, self).__init__(*args, **kwargs)
+        self._move_callback = self._extract_pixel
+        self._press_callback = self._on_press
+        self._release_callback = self._on_release
+        self._derived = None
+
+        self._line_x = self.viewer.axes.axvline(0, color='blue')
+        self._line_x.set_visible(False)
+
+        self._line_y = self.viewer.axes.axhline(0, color='blue')
+        self._line_y.set_visible(False)
+
+    def _on_press(self, mode):
+        self._pressed = True
+        self._extract_pixel(mode)
+
+    def _on_release(self, mode):
+        self._pressed = False
+
+    def _extract_pixel(self, mode):
+
+        x, y = self._event_xdata, self._event_ydata
+
+        if x is None or y is None:
+            return None
+
+        xi = int(round(x))
+        yi = int(round(y))
+
+        indices = [None] * self.viewer.state.reference_data.ndim
+        indices[self.viewer.state.x_att.axis] = xi
+        indices[self.viewer.state.y_att.axis] = yi
+
+        self._line_x.set_data([x, x], [0, 1])
+        self._line_x.set_visible(True)
+        self._line_y.set_data([0, 1], [y, y])
+        self._line_y.set_visible(True)
+        self.viewer.axes.figure.canvas.draw()
+
+        if self._derived is None:
+            self._derived = IndexedData(self.viewer.state.reference_data, indices)
+            self.viewer.session.data_collection.append(self._derived)
+        else:
+            try:
+                self._derived.indices = indices
+            except TypeError:
+                self.viewer.session.data_collection.remove(self._derived)
+                self._derived = IndexedData(self.viewer.state.reference_data, indices)
+                self.viewer.session.data_collection.append(self._derived)