class EmulatorPreferencesPane(PreferencesPane):
""" The preferences pane for the Framework application.
"""
#### 'PreferencesPane' interface ##########################################
# The factory to use for creating the preferences model object.
model_factory = EmulatorPreferences
category = Str('Editors')
#### 'FrameworkPreferencesPane' interface ################################
# Note the quirk in the RangeEditor: specifying a custom editor is
# supposed to take the defaults from the item name specified, but I
# can't get it to work with only the "mode" parameter. I have to specify
# all the other params, and the low/high values have to be attributes
# in EmulatorPreferences, not the values in the trait itself. See
# traitsui/editors/range_editor.py
view = View(
VGroup(HGroup(Item('map_width', editor=RangeEditor(mode="spinner", is_float=False, low_name='map_width_low', high_name='map_width_high')),
Label('Default Character Map Width (in bytes)'),
show_labels = False),
HGroup(Item('bitmap_width', editor=RangeEditor(mode="spinner", is_float=False, low_name='bitmap_width_low', high_name='bitmap_width_high')),
Label('Default Bitmap Width (in bytes)'),
show_labels = False),
HGroup(Item('hex_grid_width', editor=RangeEditor(mode="spinner", is_float=False, low_name='hex_grid_width_low', high_name='hex_grid_width_high')),
Label('Default Hex Grid Width (in bytes)'),
show_labels = False),
HGroup(Item('text_font'),
Label('Hex Display Font'),
show_labels = False),
HGroup(Item('header_font'),
Label('Column Header Font'),
show_labels = False),
HGroup(Item('int_display_format'),
Label('Number Display Format'),
show_labels=False),
HGroup(Item('hex_display_format'),
Label('Hex Display Format'),
show_labels=False),
HGroup(Item('hex_grid_lower_case'),
Label('Use Lower Case for Hex Digits'),
show_labels = False),
HGroup(Item('assembly_lower_case'),
Label('Use Lower Case for Assembler Mnemonics'),
show_labels = False),
HGroup(Item('highlight_background_color', editor=ColorEditor(), style='custom'),
Label('Highlight Color'),
show_labels = False),
label='Hex Editor'),
resizable=True)
class Align(HasTraits):
# The position of the view
position = Array(shape=(3, ))
brightness = Range(-2., 2., value=0.)
contrast = Range(0., 3., value=1.)
opacity = Range(0., 1., value=.1)
colormap = Enum(*lut_manager.lut_mode_list())
fliplut = Bool
outlines_visible = Bool(default_value=True)
outline_rep = Enum(outline_reps)
outline_color = Color(
default=options.config.get("mayavi_aligner", "outline_color"))
line_width = Range(0.5,
10.,
value=float(
options.config.get("mayavi_aligner", "line_width")))
point_size = Range(0.5,
10.,
value=float(
options.config.get("mayavi_aligner", "point_size")))
epi_filter = Enum(None, "median", "gradient")
filter_strength = Range(1, 20, value=3)
scene_3d = Instance(MlabSceneModel, ())
scene_x = Instance(MlabSceneModel, ())
scene_y = Instance(MlabSceneModel, ())
scene_z = Instance(MlabSceneModel, ())
# The data source
epi_src = Instance(Source)
surf_src = Instance(Source)
xfm = Instance(Filter)
surf = Instance(Module)
disable_render = Bool
flip_fb = Bool
flip_lr = Bool
flip_ud = Bool
save_callback = Instance(types.FunctionType)
save_btn = Button(label="Save Transform")
legend = Str(legend)
#---------------------------------------------------------------------------
# Object interface
#---------------------------------------------------------------------------
def __init__(self, pts, polys, epi, xfm=None, xfmtype='magnet', **traits):
'''
Parameters
----------
xfm : array_like, optional
The initial 4x4 rotation matrix into magnet space
(epi with slice affine)
'''
self.load_epi(epi, xfm, xfmtype)
self.pts, self.polys = pts, polys
self._undolist = []
self._redo = None
super(Align, self).__init__(**traits)
def load_epi(self, epifilename, xfm=None, xfmtype="magnet"):
"""Loads the EPI image from the specified epifilename.
"""
nii = nibabel.load(epifilename)
self.epi_file = nii
epi = nii.get_data().astype(float).squeeze()
if epi.ndim > 3:
epi = epi[:, :, :, 0]
self.affine = nii.get_affine()
base = nii.get_header().get_base_affine()
self.base = base
self.origin = base[:3, -1]
self.spacing = np.diag(base)[:3]
if xfm is None:
self.startxfm = np.dot(base, np.linalg.inv(self.affine))
elif xfmtype == "magnet":
self.startxfm = np.dot(np.dot(base, np.linalg.inv(self.affine)),
xfm)
else:
print("using xfmtype %s" % xfmtype)
self.startxfm = xfm
self.center = self.spacing * nii.get_shape()[:3] / 2 + self.origin
self.padshape = 2**(np.ceil(np.log2(np.array(epi.shape))))
epi = np.nan_to_num(epi)
self.epi_orig = epi - epi.min()
self.epi_orig /= self.epi_orig.max()
self.epi_orig *= 2
self.epi_orig -= 1
self.epi = self.epi_orig.copy()
#---------------------------------------------------------------------------
# Default values
#---------------------------------------------------------------------------
def _position_default(self):
return np.abs(self.origin) + (
(np.array(self.epi.shape) + 1) % 2) * np.abs(self.spacing) / 2
def _epi_src_default(self):
sf = mlab.pipeline.scalar_field(self.epi,
figure=self.scene_3d.mayavi_scene,
name='EPI')
sf.origin = self.origin
sf.spacing = self.spacing
return sf
def _surf_src_default(self):
return mlab.pipeline.triangular_mesh_source(
self.pts[:, 0],
self.pts[:, 1],
self.pts[:, 2],
self.polys,
figure=self.scene_3d.mayavi_scene,
name='Cortex')
def _surf_default(self):
smooth = mlab.pipeline.poly_data_normals(
self.xfm, figure=self.scene_3d.mayavi_scene)
smooth.filter.splitting = False
surf = mlab.pipeline.surface(smooth, figure=self.scene_3d.mayavi_scene)
surf.actor.mapper.scalar_visibility = 0
return surf
def _xfm_default(self):
xfm = mlab.pipeline.transform_data(self.surf_src,
figure=self.scene_3d.mayavi_scene)
def savexfm(info, evt):
self._undolist.append(xfm.transform.matrix.to_array())
np.save("/tmp/last_xfm.npy", self.get_xfm())
xfm.widget.add_observer("EndInteractionEvent", savexfm)
xfm.widget.add_observer("EndInteractionEvent", self.update_slabs)
xfm.transform.set_matrix(self.startxfm.ravel())
xfm.widget.set_transform(xfm.transform)
return xfm
#---------------------------------------------------------------------------
# Scene activation callbacks
#---------------------------------------------------------------------------
@on_trait_change('scene_3d.activated')
def display_scene_3d(self):
self.scene_3d.mlab.view(40, 50)
self.scene_3d.scene.renderer.use_depth_peeling = True
self.scene_3d.scene.background = (0, 0, 0)
# Keep the view always pointing up
self.scene_3d.scene.interactor.interactor_style = tvtk.InteractorStyleTerrain(
)
self.scene_3d.scene_editor.aligner = self
self.opacity = float(options.config.get("mayavi_aligner", "opacity"))
self.xfm.widget.enabled = False
self.colormap = options.config.get("mayavi_aligner", "colormap")
self.disable_render = True
for ax in [self.x_axis, self.y_axis, self.z_axis]:
ax.update_position()
ax.reset_view()
self.disable_render = False
@on_trait_change('scene_x.activated')
def display_scene_x(self):
self.x_axis = XAxis(parent=self)
@on_trait_change('scene_y.activated')
def display_scene_y(self):
self.y_axis = YAxis(parent=self)
@on_trait_change('scene_z.activated')
def display_scene_z(self):
self.z_axis = ZAxis(parent=self)
#---------------------------------------------------------------------------
# Traits callback
#---------------------------------------------------------------------------
def _save_btn_changed(self):
if self.save_callback is not None:
self.save_callback(self)
def _disable_render_changed(self):
self.scene_3d.scene.disable_render = self.disable_render
def _position_changed(self):
self.disable_render = True
for ax in [self.x_axis, self.y_axis, self.z_axis]:
ax.update_position()
self.disable_render = False
def _outlines_visible_changed(self):
self.disable_render = True
for ax in [self.x_axis, self.y_axis, self.z_axis]:
ax.toggle_outline()
self.disable_render = False
@on_trait_change("colormap, fliplut")
def update_colormap(self):
for ax in [self.x_axis, self.y_axis, self.z_axis]:
if ax.ipw_3d and ax.ipw:
ax.ipw_3d.parent.scalar_lut_manager.set(
lut_mode=self.colormap, reverse_lut=self.fliplut)
ax.ipw.parent.scalar_lut_manager.set(lut_mode=self.colormap,
reverse_lut=self.fliplut)
def _opacity_changed(self):
self.surf.actor.property.opacity = self.opacity
@on_trait_change("brightness,contrast")
def update_brightness(self):
self.epi_src.scalar_data = (self.epi * self.contrast) + self.brightness
@on_trait_change("flip_ud")
def update_flipud(self):
#self.epi_src.scalar_data = self.epi_src.scalar_data[:,:,::-1]
flip = np.eye(4)
flip[2, 2] = -1
mat = self.xfm.transform.matrix.to_array()
self.set_xfm(np.dot(mat, flip), "base")
@on_trait_change("flip_lr")
def update_fliplr(self):
#self.epi_src.scalar_data = self.epi_src.scalar_data[::-1]
flip = np.eye(4)
flip[0, 0] = -1
mat = self.xfm.transform.matrix.to_array()
self.set_xfm(np.dot(mat, flip), "base")
@on_trait_change("flip_fb")
def update_flipfb(self):
#self.epi_src.scalar_data = self.epi_src.scalar_data[:,::-1]
flip = np.eye(4)
flip[1, 1] = -1
mat = self.xfm.transform.matrix.to_array()
self.set_xfm(np.dot(mat, flip), "base")
@on_trait_change("epi_filter, filter_strength")
def update_epifilter(self):
if self.epi_filter is None:
self.epi = self.epi_orig.copy()
elif self.epi_filter == "median":
fstr = np.floor(self.filter_strength / 2) * 2 + 1
self.epi = volume.detrend_median(self.epi_orig.T, fstr).T
elif self.epi_filter == "gradient":
self.epi = volume.detrend_gradient(self.epi_orig.T,
self.filter_strength).T
self.update_brightness()
def update_slabs(self, *args, **kwargs):
self.disable_render = True
for ax in [self.x_axis, self.y_axis, self.z_axis]:
ax.update_slab()
self.disable_render = False
def get_xfm(self, xfmtype="magnet"):
if xfmtype in ["anat->epicoord", "coord"]:
ibase = np.linalg.inv(self.base)
xfm = self.xfm.transform.matrix.to_array()
return np.dot(ibase, xfm)
elif xfmtype in ["anat->epibase", "base"]:
return self.xfm.transform.matrix.to_array()
elif xfmtype in ['anat->magnet', "magnet"]:
ibase = np.linalg.inv(self.base)
xfm = self.xfm.transform.matrix.to_array()
return np.dot(self.affine, np.dot(ibase, xfm))
def set_xfm(self, matrix, xfmtype='magnet'):
assert xfmtype in "magnet coord base".split(), "Unknown transform type"
if xfmtype == "coord":
matrix = np.dot(self.base, matrix)
elif xfmtype == "magnet":
iaff = np.linalg.inv(self.affine)
matrix = np.dot(self.base, np.dot(iaff, matrix))
self.xfm.transform.set_matrix(matrix.ravel())
self.xfm.widget.set_transform(self.xfm.transform)
self.xfm.update_pipeline()
self.update_slabs()
def undo(self):
if len(self._undolist) > 0:
self.xfm.transform.set_matrix(self._undolist[-1].ravel())
self.xfm.widget.set_transform(self.xfm.transform)
self.xfm.update_pipeline()
self.update_slabs()
self._redo = self._undolist.pop()
#---------------------------------------------------------------------------
# The layout of the dialog created
#---------------------------------------------------------------------------
view = View(HGroup(
Group(
Item('scene_y', editor=SceneEditor(scene_class=FlatScene)),
Item('scene_z', editor=SceneEditor(scene_class=FlatScene)),
show_labels=False,
),
Group(
Item('scene_x', editor=SceneEditor(scene_class=FlatScene)),
Item('scene_3d', editor=SceneEditor(scene_class=ThreeDScene)),
show_labels=False,
),
Group(Group(
Item("save_btn",
show_label=False,
visible_when="save_callback is not None"),
"brightness",
"contrast",
"epi_filter",
Item('filter_strength', visible_when="epi_filter is not None"),
"_",
"opacity",
"_",
Item('colormap',
editor=ImageEnumEditor(values=lut_manager.lut_mode_list(),
cols=6,
path=lut_manager.lut_image_dir)),
"fliplut",
"_",
"flip_ud",
"flip_lr",
"flip_fb",
"_",
Item('outline_color', editor=ColorEditor()),
'outline_rep',
'line_width',
'point_size',
'_',
),
Group(
Item('legend',
editor=TextEditor(),
style='readonly',
show_label=False,
emphasized=True,
dock='vertical'),
show_labels=False,
),
orientation='vertical'),
),
resizable=True,
title='Aligner')
class Polygon(HasTraits):
line_color = Trait(Color((0, 0, 0)), editor=ColorEditor())
class Polygon(HasTraits):
line_color = Trait(wx.wxColour(0, 0, 0), editor=ColorEditor())
class multicolorfits_viewer(HasTraits):
"""The main window. Has instructions for creating and destroying the app.
"""
panel1 = Instance(ControlPanel)
panel2 = Instance(ControlPanel)
panel3 = Instance(ControlPanel)
panel4 = Instance(ControlPanel)
figure_combined = Instance(Figure, ())
image = Array()
image_axes = Instance(Axes)
image_axesimage = Instance(AxesImage)
image_xsize = Int(256)
image_ysize = Int(256)
gamma = Float(2.2)
tickcolor = Str(
'0.9'
) #,auto_set=False,enter_set=True) #Apparently need to set to TextEditor explicitly below...
tickcolor_picker = ColorTrait((230, 230, 230))
sexdec = Enum('Sexagesimal', 'Decimal')
plotbutton_combined = Button(u"Plot Combined")
plotbutton_inverted_combined = Button(u"Plot Inverted Combined")
clearbutton_combined = Button(u"Clear Combined")
save_the_image = Button(u"Save Image")
save_the_fits = Button(u"Save RGB Fits")
print_params = Button(u"Print Params")
status_string_left = Str('')
status_string_right = Str('')
def _panel1_default(self):
return ControlPanel() #figure=self.figure)
def _panel2_default(self):
return ControlPanel() #figure=self.figure)
def _panel3_default(self):
return ControlPanel() #figure=self.figure)
def _panel4_default(self):
return ControlPanel() #figure=self.figure)
def __init__(self):
super(multicolorfits_viewer, self).__init__()
self._init_params(
) #Set placeholder things like the WCS, tick color, map units...
self.image = self._fresh_image() #Sets a blank image
self.image_axes = self.figure_combined.add_subplot(111, aspect=1)
self.image_axesimage = self.image_axes.imshow(self.image,
cmap='gist_gray',
origin='lower',
interpolation='nearest')
self.image_axes.set_xlabel(self.xlabel)
self.image_axes.set_ylabel(self.ylabel)
self.image_axes.tick_params(
axis='both',
color=self.tickcolor) #colors=... also sets label color
try:
self.image_axes.coords.frame.set_color(
self.tickcolor
) #Updates the frame color. .coords won't exist until WCS set
except:
[
self.image_axes.spines[s].set_color(self.tickcolor)
for s in ['top', 'bottom', 'left', 'right']
]
view = View(Item("gamma",label=u"Gamma",show_label=True),
Item('_'),
HSplit(
Group(
Group(Item('panel1', style="custom",show_label=False),label='Image 1'),
Group(Item('panel2', style="custom",show_label=False),label='Image 2'),
Group(Item('panel3', style="custom",show_label=False),label='Image 3'),
Group(Item('panel4', style="custom",show_label=False),label='Image 4'),
orientation='horizontal',layout='tabbed',springy=True),
VGroup(
HGroup(
Item('tickcolor',label='Tick Color',show_label=True, \
tooltip='Color of ticks: standard name float[0..1], or #hex', \
editor=TextEditor(auto_set=False, enter_set=True,)),
Item('tickcolor_picker',label='Pick',show_label=True,editor=ColorEditor()),
Item('sexdec',label='Coordinate Style',tooltip=u'Display coordinates in sexagesimal or decimal', \
show_label=True),
),
Item('figure_combined', editor=MPLFigureEditor(),show_label=False, width=900, height=800,resizable=True),
HGroup(
Item('plotbutton_combined', tooltip=u"Plot the image",show_label=False),
Item('plotbutton_inverted_combined', tooltip=u"Plot the inverted image",show_label=False),
Item('clearbutton_combined',tooltip=u'Clear the combined figure',show_label=False),
Item("save_the_image", tooltip=u"Save current image. Mileage may vary...",show_label=False),
Item("save_the_fits", tooltip=u"Save RGB frames as single fits file with header.",show_label=False),
Item("print_params", tooltip=u"Print out current settings for use in manual image scripting.",show_label=False),
), #HGroup
), #VGroup
show_labels=False,),
resizable=True,
height=0.75, width=0.75,
statusbar = [StatusItem(name = 'status_string_left', width = 0.5),
StatusItem(name = 'status_string_right', width = 0.5)],
title=u"Fits Multi-Color Combiner",handler=MPLInitHandler ) #View
def _init_params(self):
plt.rcParams.update({'font.family': 'serif','xtick.major.size':6,'ytick.major.size':6, \
'xtick.major.width':1.,'ytick.major.width':1., \
'xtick.direction':'in','ytick.direction':'in'})
try:
plt.rcParams.update({
'xtick.top': True,
'ytick.right': True
}) #apparently not in mpl v<2.0...
except:
pass #Make a workaround for mpl<2.0 later...
self.datamin_initial = 0.
self.datamax_initial = 1.
self.datamin = 0.
self.datamax = 1. #This will be the displayed value of the scaling min/max
#self.mapunits='Pixel Value'
#self.tickcolor='0.5'#'white', 'black', '0.5'
self.wcs = WCS()
self.xlabel = 'x'
self.ylabel = 'y'
def _fresh_image(self):
#self.norm=ImageNormalize(self.image,stretch=scaling_fns['linear']() )
blankdata = np.zeros([100, 100])
blankdata[-1, -1] = 1
return blankdata
def update_radecpars(self):
self.rapars = self.image_axes.coords[0]
self.decpars = self.image_axes.coords[1]
self.rapars.set_ticks(color=self.tickcolor)
self.decpars.set_ticks(color=self.tickcolor)
self.rapars.set_ticks(number=6)
self.decpars.set_ticks(number=6)
#self.rapars.set_ticklabel(size=8); self.decpars.set_ticklabel(size=8); #size here means the tick length
##self.rapars.set_ticks(spacing=10*u.arcmin, color='white', exclude_overlapping=True)
##self.decpars.set_ticks(spacing=5*u.arcmin, color='white', exclude_overlapping=True)
self.rapars.display_minor_ticks(True)
#self.rapars.set_minor_frequency(10)
self.decpars.display_minor_ticks(True)
if self.sexdec == 'Sexagesimal':
self.rapars.set_major_formatter('hh:mm:ss.ss')
self.decpars.set_major_formatter('dd:mm:ss.ss')
#self.rapars.set_separator(('$^\mathrm{H}$', "'", '"'))
self.rapars.set_separator(('H ', "' ", '" '))
#format_xcoord=lambda x,y: '{}i$^\mathrm{H}${}{}{}'.format(x[0],x[1],"'",x[2],'"')
#self.image_axes.format_coord=format_xcoord
else:
self.rapars.set_major_formatter('d.dddddd')
self.decpars.set_major_formatter('d.dddddd')
##self.decpars.ticklabels.set_rotation(45) #Rotate ticklabels
##self.decpars.ticklabels.set_color(xkcdrust) #Ticklabel Color
@on_trait_change('tickcolor')
def update_tickcolor(self):
try:
#Catch case when you've predefined a color variable in hex string format, e.g., mynewred='#C11B17'
#--> Need to do this first, otherwise traits throws a fit up the stack even despite the try/except check
globals()[
self.tickcolor] #This check should catch undefined inputs
self.image_axes.tick_params(axis='both',
color=globals()[self.tickcolor])
self.image_axes.coords.frame.set_color(self.tickcolor)
self.tickcolor_picker = hex_to_rgb(globals()[self.tickcolor])
self.status_string_right = 'Tick color changed to ' + self.tickcolor
except:
try:
self.tickcolor = to_hex(self.tickcolor)
try:
self.update_radecpars()
except:
self.image_axes.tick_params(axis='both',
color=to_hex(self.tickcolor))
self.image_axes.coords.frame.set_color(
to_hex(self.tickcolor))
self.status_string_right = 'Tick color changed to ' + self.tickcolor
except:
self.status_string_right = "Color name %s not recognized. Must be standard mpl.colors string, float[0..1] or #hex string" % (
self.tickcolor)
try:
self.tickcolor_picker = hex_to_rgb(to_hex(
self.tickcolor)) #update the picker color...
except:
pass
self.figure_combined.canvas.draw()
@on_trait_change('tickcolor_picker')
def update_tickcolorpicker(self):
#print self.tickcolor_picker.name()
self.tickcolor = self.tickcolor_picker.name()
@on_trait_change('sexdec')
def update_sexdec(self):
self.update_radecpars()
self.figure_combined.canvas.draw()
self.status_string_right = 'Coordinate style changed to ' + self.sexdec
def _plotbutton_combined_fired(self):
try:
self.panel1.data
except:
self.status_string_right = "No fits file loaded yet!"
return
#self.image=self.panel1.data
self.wcs = WCS(self.panel1.hdr)
self.hdr = self.panel1.hdr
self.combined_RGB = combine_multicolor([
pan.image_colorRGB
for pan in [self.panel1, self.panel2, self.panel3, self.panel4]
if pan.in_use == True
],
gamma=self.gamma)
###Using this command is preferable, as long as the projection doesn't need to be updated...
# The home zoom button will work, but no WCS labels because projection wasn't set during init.
#self.image_axesimage.set_data(self.data)
###Using this set instead properly updates the axes labels to WCS, but the home zoom button won't work
self.figure_combined.clf()
self.image_axes = self.figure_combined.add_subplot(111,
aspect=1,
projection=self.wcs)
self.image_axesimage = self.image_axes.imshow(self.combined_RGB,
origin='lower',
interpolation='nearest')
self.update_radecpars()
self.figure_combined.canvas.draw()
self.status_string_right = "Plot updated"
def _plotbutton_inverted_combined_fired(self):
try:
self.panel1.data
except:
self.status_string_right = "No fits file loaded yet!"
return
self.wcs = WCS(self.panel1.hdr)
self.hdr = self.panel1.hdr
self.combined_RGB = combine_multicolor(
[
pan.image_colorRGB for pan in
[self.panel1, self.panel2, self.panel3, self.panel4]
if pan.in_use == True
],
inverse=True,
gamma=self.gamma,
)
self.figure_combined.clf()
self.image_axes = self.figure_combined.add_subplot(111,
aspect=1,
projection=self.wcs)
self.image_axesimage = self.image_axes.imshow(self.combined_RGB,
origin='lower',
interpolation='nearest')
self.update_radecpars()
self.figure_combined.canvas.draw()
self.status_string_right = "Plot updated"
def _clearbutton_combined_fired(self):
try:
del self.combined_RGB #If clear already pressed once, data will already have been deleted...
except:
pass
self.in_use = False
self.figure_combined.clf()
self.image = self._fresh_image()
self.image_axes = self.figure_combined.add_subplot(111, aspect=1)
self.image_axesimage = self.image_axes.imshow(self.image,
cmap='gist_gray',
origin='lower',
interpolation='nearest')
self.xlabel = 'x'
self.ylabel = 'y'
self.image_axes.set_xlabel(self.xlabel)
self.image_axes.set_ylabel(self.ylabel)
self.image_axes.tick_params(axis='both', color=self.tickcolor)
try:
self.image_axes.coords.frame.set_color(self.tickcolor)
except:
self.tickcolor_picker = hex_to_rgb(to_hex(self.tickcolor))
self.figure_combined.canvas.draw()
self.status_string_right = "Plot cleared"
def setup_mpl_events(self):
self.image_axeswidget = AxesWidget(self.image_axes)
self.image_axeswidget.connect_event('motion_notify_event',
self.image_on_motion)
self.image_axeswidget.connect_event('figure_leave_event',
self.on_cursor_leave)
self.image_axeswidget.connect_event('figure_enter_event',
self.on_cursor_enter)
self.image_axeswidget.connect_event('button_press_event',
self.image_on_click)
def image_on_motion(self, event):
if event.xdata is None or event.ydata is None: return
x = int(np.round(event.xdata))
y = int(np.round(event.ydata))
if ((x >= 0) and (x < self.image.shape[1]) and (y >= 0)
and (y < self.image.shape[0])):
imval = self.image[y, x]
self.status_string_left = "x,y={},{} {:.5g}".format(x, y, imval)
else:
self.status_string_left = ""
def image_on_click(self, event):
if event.xdata is None or event.ydata is None or event.button is not 1:
return #Covers when click outside of main plot
#print event
x = int(
np.round(event.xdata)
) #xdata is the actual pixel position. xy is in 'display space', i.e. pixels in the canvas
y = int(np.round(event.ydata))
xwcs, ywcs = self.wcs.wcs_pix2world([[x, y]], 0)[0]
#print xwcs,ywcs
if ((x >= 0) and (x < self.image.shape[1]) and (y >= 0)
and (y < self.image.shape[0])):
imval = self.image[y, x]
self.status_string_right = "x,y=[{},{}], RA,DEC=[{}, {}], value = {:.5g}".format(
x, y, xwcs, ywcs, imval)
#self.status_string_right = "x,y[{},{}] = {:.3f},{:.3f} {:.5g}".format(x, y,event.xdata,event.ydata, imval)
else:
self.status_string_right = ""
## left-click: event.button = 1, middle-click: event.button=2, right-click: event.button=3.
## For double-click, event.dblclick = False for first click, True on second
#print event.button, event.dblclick
def on_cursor_leave(self, event):
QApplication.restoreOverrideCursor()
self.status_string_left = ''
def on_cursor_enter(self, event):
QApplication.setOverrideCursor(Qt.CrossCursor)
def _save_the_image_fired(self):
dlg = FileDialog(action='save as')
if dlg.open() == OK: plt.savefig(dlg.path, size=(800, 800), dpi=300)
def _save_the_fits_fired(self):
#Generate a generic header with correct WCS and comments about the colors that made it
#... come back and finish this later...
dlg = FileDialog(action='save as')
if dlg.open() == OK:
pyfits.writeto(
dlg.path,
np.swapaxes(np.swapaxes(self.combined_RGB, 0, 2), 2, 1),
self.hdr)
def _print_params_fired(self):
print('\n\nRGB Image plot params:')
pan_i = 0
for pan in [self.panel1, self.panel2, self.panel3, self.panel4]:
pan_i += 1
if pan.in_use == True:
print('image%i: ' % (pan_i))
print(' vmin = %.3e , vmax = %.3e, scale = %s' %
(pan.datamin, pan.datamax, pan.image_scale))
print(" image color = '%s'" % (pan.imagecolor))
print("gamma = %.1f , tick color = '%s'\n" %
(self.gamma, self.tickcolor))
class ControlPanel(HasTraits):
"""This is the control panel where the various parameters for the images are specified
"""
gamma = 2.2
fitsfile = File(filter=[u"*.fits"])
image_figure = Instance(Figure, ())
image = Array()
image_axes = Instance(Axes)
image_axesimage = Instance(AxesImage)
image_xsize = Int(256)
image_ysize = Int(256)
datamin = Float(0.0, auto_set=False, enter_set=True) #Say, in mJy
datamax = Float(
1.0, auto_set=False, enter_set=True
) #auto_set=input set on each keystroke, enter_set=set after Enter
percent_min = Range(value=0.0, low=0.0, high=100.)
percent_max = Range(value=100.0, low=0.0,
high=100.) #Percentile of data values for rescaling
minmaxbutton = Button('Min/Max')
zscalebutton = Button('Zscale')
image_scale = Str('linear')
scale_dropdown = Enum(
['linear', 'sqrt', 'squared', 'log', 'power', 'sinh', 'asinh'])
imagecolor = Str('#FFFFFF')
imagecolor_picker = ColorTrait((255, 255, 255))
#plotbeam_button=Button('Add Beam (FWHM)')
plotbutton_individual = Button(u"Plot Single")
plotbutton_inverted_individual = Button(u"Plot Inverted Single")
clearbutton_individual = Button(u"Clear Single")
status_string_left = Str('')
status_string_right = Str('')
def __init__(self):
self._init_params(
) #Set placeholder things like the WCS, tick color, map units...
self.image = self._fresh_image() #Sets a blank image
self.image_axes = self.image_figure.add_subplot(111, aspect=1)
self.image_axesimage = self.image_axes.imshow(self.image,
cmap='gist_gray',
origin='lower',
interpolation='nearest')
self.image_axes.axis('off')
view = View(
HSplit(
VGroup(
Item("fitsfile", label=u"Select 2D FITS file", show_label=True), #,height=100),
HGroup(
VGroup(
Item('plotbutton_individual', tooltip=u"Plot the single image",show_label=False),
Item('plotbutton_inverted_individual', tooltip=u"Plot the single inverted image",show_label=False),
Item('clearbutton_individual', tooltip=u"Clear the single image",show_label=False),
Item('_'),
Item('imagecolor',label='Image Color',show_label=True, \
tooltip='Color of ticks: standard name float[0..1], or #hex', \
editor=TextEditor(auto_set=False, enter_set=True,)),
Item('imagecolor_picker',label='Pick',show_label=True,editor=ColorEditor()),
),
Item('image_figure', editor=MPLFigureEditor(), show_label=False, width=300, height=300,resizable=True),
),
HGroup(Item('datamin', tooltip=u"Minimum data val for scaling", show_label=True),
Item('datamax', tooltip=u"Maximum data val for scaling", show_label=True)),
Item('percent_min', tooltip=u"Min. percentile for scaling", show_label=True),
Item('percent_max', tooltip=u"Max. percentile for scaling", show_label=True),
HGroup(Item('minmaxbutton', tooltip=u"Reset to data min/max", show_label=False),
Item('zscalebutton', tooltip=u"Compute scale min/max from zscale algorithm", show_label=False)),
Item('scale_dropdown',label='Scale',show_label=True),
), #End of Left column
), #End of HSplit
resizable=True, #height=0.75, width=0.75, #title=u"Multi-Color Image Combiner",
handler=MPLInitHandler,
statusbar = [StatusItem(name = 'status_string_left', width = 0.5), StatusItem(name = 'status_string_right', width = 0.5)]
) #End of View
def _init_params(self):
self.in_use = False
plt.rcParams.update({'font.family': 'serif','xtick.major.size':6,'ytick.major.size':6, \
'xtick.major.width':1.,'ytick.major.width':1., \
'xtick.direction':'in','ytick.direction':'in'})
try:
plt.rcParams.update({
'xtick.top': True,
'ytick.right': True
}) #apparently not in mpl v<2.0...
except:
pass #Make a workaround for mpl<2.0 later...
self.datamin_initial = 0.
self.datamax_initial = 1.
self.datamin = 0.
self.datamax = 1. #This will be the displayed value of the scaling min/max
def _fresh_image(self):
blankdata = np.zeros([100, 100])
blankdata[-1, -1] = 1
return blankdata
def _fitsfile_changed(self):
self.data, self.hdr = pyfits.getdata(self.fitsfile, header=True)
force_hdr_floats(
self.hdr
) #Ensure that WCS cards such as CDELT are floats instead of strings
naxis = int(self.hdr['NAXIS'])
if naxis > 2:
#print('Dropping Extra axes')
self.hdr = force_hdr_to_2D(self.hdr)
try:
self.data = self.data[0, 0, :, :]
except:
self.data = self.data[0, :, :]
self.status_string_right = 'Dropped extra axes'
self.datamax_initial = np.asscalar(np.nanmax(self.data))
self.datamin_initial = np.asscalar(np.nanmin(self.data))
self.datamax = np.asscalar(np.nanmax(self.data))
self.datamin = np.asscalar(np.nanmin(self.data))
self.in_use = True
#@on_trait_change('imagecolor')
#def update_imagecolor(self):
def _imagecolor_changed(self):
try:
#Catch case when you've predefined a color variable in hex string format, e.g., mynewred='#C11B17'
#--> Need to do this first, otherwise traits throws a fit up the stack even despite the try/except check
globals()[
self.imagecolor] #This check should catch undefined inputs
self.imagecolor_picker = hex_to_rgb(globals()[self.imagecolor])
self.status_string_right = 'Image color changed to ' + self.imagecolor
except:
try:
self.imagecolor = to_hex(self.imagecolor)
self.status_string_right = 'Image color changed to ' + self.imagecolor
except:
self.status_string_right = "Color name %s not recognized. Must be standard mpl.colors string, float[0..1] or #hex string" % (
self.imagecolor)
try:
self.imagecolor_picker = hex_to_rgb(to_hex(
self.imagecolor)) #update the picker color...
except:
pass
### self.image_greyRGB and self.image_colorRGB may not yet be instantiated if the color is changed before clicking 'plot'
try:
self.image_colorRGB = colorize_image(self.image_greyRGB,
self.imagecolor,
colorintype='hex',
gammacorr_color=self.gamma)
except:
pass
try:
self.image_axesimage.set_data(self.image_colorRGB**(1. /
self.gamma))
except:
pass
self.in_use = True
self.image_figure.canvas.draw()
#@on_trait_change('imagecolor_picker')
#def update_imagecolorpicker(self):
def _imagecolor_picker_changed(self):
#print self.tickcolor_picker.name()
self.imagecolor = self.imagecolor_picker.name()
#@on_trait_change('percent_min')
#def update_scalepercmin(self):
def _percent_min_changed(self):
self.datamin = np.nanpercentile(self.data, self.percent_min)
self.data_scaled = (
scaling_fns[self.image_scale]() +
ManualInterval(vmin=self.datamin, vmax=self.datamax))(self.data)
self.image_greyRGB = ski_color.gray2rgb(
adjust_gamma(self.data_scaled, self.gamma))
self.image_colorRGB = colorize_image(self.image_greyRGB,
self.imagecolor,
colorintype='hex',
gammacorr_color=self.gamma)
self.image_axesimage.set_data(self.image_colorRGB**(1. / self.gamma))
self.image_figure.canvas.draw()
self.status_string_right = "Updated scale using percentiles"
#@on_trait_change('percent_max')
#def update_scalepercmax(self):
def _percent_max_changed(self):
self.datamax = np.nanpercentile(self.data, self.percent_max)
self.data_scaled = (
scaling_fns[self.image_scale]() +
ManualInterval(vmin=self.datamin, vmax=self.datamax))(self.data)
self.image_greyRGB = ski_color.gray2rgb(
adjust_gamma(self.data_scaled, self.gamma))
self.image_colorRGB = colorize_image(self.image_greyRGB,
self.imagecolor,
colorintype='hex',
gammacorr_color=self.gamma)
self.image_axesimage.set_data(self.image_colorRGB**(1. / self.gamma))
self.image_figure.canvas.draw()
self.status_string_right = "Updated scale using percentiles"
### Very slow to update datamin and datamax as well as percs... Can comment these if desired and just hit plot after datamin
#@on_trait_change('datamin')
#def update_datamin(self): self.percent_min=np.round(percentileofscore(self.data.ravel(),self.datamin,kind='strict'),2)
def _datamin_changed(self):
self.percent_min = np.round(
percentileofscore(self.data.ravel(), self.datamin, kind='strict'),
2)
#@on_trait_change('datamax')
#def update_datamax(self): self.percent_max=np.round(percentileofscore(self.data.ravel(),self.datamax,kind='strict'),2)
def _datamax_changed(self):
self.percent_max = np.round(
percentileofscore(self.data.ravel(), self.datamax, kind='strict'),
2)
#@on_trait_change('scale_dropdown')
#def update_image_scale(self):
def _scale_dropdown_changed(self):
self.image_scale = self.scale_dropdown
#self.norm=ImageNormalize(self.sregion,stretch=scaling_fns[self.image_scale]() )
self.data_scaled = (
scaling_fns[self.image_scale]() +
ManualInterval(vmin=self.datamin, vmax=self.datamax))(self.data)
#*** Instead, should I just integrate my imscale class here instead of astropy? ...
self.image_greyRGB = ski_color.gray2rgb(
adjust_gamma(self.data_scaled, self.gamma))
self.image_colorRGB = colorize_image(self.image_greyRGB,
self.imagecolor,
colorintype='hex',
gammacorr_color=self.gamma)
self.image_axesimage.set_data(self.image_colorRGB**(1. / self.gamma))
self.in_use = True
self.image_figure.canvas.draw()
self.status_string_right = 'Image scale function changed to ' + self.image_scale
def _minmaxbutton_fired(self):
self.datamin = self.datamin_initial
self.datamax = self.datamax_initial
#self.image_axesimage.norm.vmin=self.datamin
#self.image_axesimage.norm.vmax=self.datamax
self.percent_min = np.round(
percentileofscore(self.data.ravel(), self.datamin, kind='strict'),
2)
self.percent_max = np.round(
percentileofscore(self.data.ravel(), self.datamax, kind='strict'),
2)
#self.image_figure.canvas.draw()
self.status_string_right = "Scale reset to min/max"
def _zscalebutton_fired(self):
tmpZscale = ZScaleInterval().get_limits(self.data)
self.datamin = float(tmpZscale[0])
self.datamax = float(tmpZscale[1])
self.percent_min = np.round(
percentileofscore(self.data.ravel(), self.datamin, kind='strict'),
2)
self.percent_max = np.round(
percentileofscore(self.data.ravel(), self.datamax, kind='strict'),
2)
#self.image_figure.canvas.draw()
self.status_string_right = "Min/max determined by zscale"
def _plotbutton_individual_fired(self):
try:
self.data
except:
self.status_string_right = "No fits file loaded yet!"
return
#self.image=self.data
###Using this command is preferable, as long as the projection doesn't need to be updated...
# The home zoom button will work, but no WCS labels because projection wasn't set during init.
#Scale the data to [0,1] range
self.data_scaled = (
scaling_fns[self.image_scale]() +
ManualInterval(vmin=self.datamin, vmax=self.datamax))(self.data)
#Convert scale[0,1] image to greyscale RGB image
self.image_greyRGB = ski_color.gray2rgb(
adjust_gamma(self.data_scaled, self.gamma))
self.image_colorRGB = colorize_image(self.image_greyRGB,
self.imagecolor,
colorintype='hex',
gammacorr_color=self.gamma)
self.image_axesimage.set_data(self.image_colorRGB**(1. / self.gamma))
###Using this set instead properly updates the axes labels to WCS, but the home zoom button won't work
#self.image_figure.clf()
#self.image_axes = self.image_figure.add_subplot(111,aspect=1)#,projection=self.wcs)
#self.image_axesimage = self.image_axes.imshow(self.image, cmap=self.image_cmap,origin='lower',interpolation='nearest', norm=self.norm)
self.percent_min = np.round(
percentileofscore(self.data.ravel(), self.datamin, kind='strict'),
2)
self.percent_max = np.round(
percentileofscore(self.data.ravel(), self.datamax, kind='strict'),
2)
self.in_use = True
#self.update_radecpars()
self.image_figure.canvas.draw()
self.status_string_right = "Plot updated"
def _plotbutton_inverted_individual_fired(self):
try:
self.data
except:
self.status_string_right = "No fits file loaded yet!"
return
self.data_scaled = (
scaling_fns[self.image_scale]() +
ManualInterval(vmin=self.datamin, vmax=self.datamax))(self.data)
self.image_greyRGB = ski_color.gray2rgb(
adjust_gamma(self.data_scaled, self.gamma))
self.image_colorRGB = colorize_image(self.image_greyRGB,
hexinv(self.imagecolor),
colorintype='hex',
gammacorr_color=self.gamma)
#self.image_axesimage.set_data(1.-self.image_colorRGB**(1./self.gamma))
self.image_axesimage.set_data(
combine_multicolor([
self.image_colorRGB,
],
gamma=self.gamma,
inverse=True))
self.percent_min = np.round(
percentileofscore(self.data.ravel(), self.datamin, kind='strict'),
2)
self.percent_max = np.round(
percentileofscore(self.data.ravel(), self.datamax, kind='strict'),
2)
self.in_use = True
self.image_figure.canvas.draw()
self.status_string_right = "Plot updated"
def _clearbutton_individual_fired(self):
try:
del self.data, self.data_scaled, self.image_greyRGB
self.image_colorRGB #In case clear already pressed once
except:
pass
self.in_use = False
self.image_figure.clf()
self.image = self._fresh_image()
self.image_axes = self.image_figure.add_subplot(111, aspect=1)
self.image_axesimage = self.image_axes.imshow(self.image,
cmap='gist_gray',
origin='lower',
interpolation='nearest')
self.image_axes.axis('off')
self.image_figure.canvas.draw()
self.status_string_right = "Plot cleared"
def setup_mpl_events(self):
self.image_axeswidget = AxesWidget(self.image_axes)
self.image_axeswidget.connect_event('motion_notify_event',
self.image_on_motion)
self.image_axeswidget.connect_event('figure_leave_event',
self.on_cursor_leave)
self.image_axeswidget.connect_event('figure_enter_event',
self.on_cursor_enter)
self.image_axeswidget.connect_event('button_press_event',
self.image_on_click)
def image_on_motion(self, event):
if event.xdata is None or event.ydata is None: return
x = int(np.round(event.xdata))
y = int(np.round(event.ydata))
if ((x >= 0) and (x < self.image.shape[1]) and (y >= 0)
and (y < self.image.shape[0])):
imval = self.image[y, x]
self.status_string_left = "x,y={},{} {:.5g}".format(x, y, imval)
else:
self.status_string_left = ""
def image_on_click(self, event):
if event.xdata is None or event.ydata is None or event.button is not 1:
return #Covers when click outside of main plot
#print event
x = int(
np.round(event.xdata)
) #xdata is the actual pixel position. xy is in 'display space', i.e. pixels in the canvas
y = int(np.round(event.ydata))
#xwcs,ywcs=self.wcs.wcs_pix2world([[x,y]],0)[0]; #print xwcs,ywcs
if ((x >= 0) and (x < self.image.shape[1]) and (y >= 0)
and (y < self.image.shape[0])):
imval = self.image[y, x]
#self.status_string_right = "x,y=[{},{}], RA,DEC=[{}, {}], value = {:.5g}".format(x, y,xwcs,ywcs, imval)
self.status_string_right = "x,y[{},{}] = {:.3f},{:.3f} {:.5g}".format(
x, y, event.xdata, event.ydata, imval)
else:
self.status_string_right = ""
## left-click: event.button = 1, middle-click: event.button=2, right-click: event.button=3.
## For double-click, event.dblclick = False for first click, True on second
#print event.button, event.dblclick
def on_cursor_leave(self, event):
QApplication.restoreOverrideCursor()
self.status_string_left = ''
def on_cursor_enter(self, event):
QApplication.setOverrideCursor(Qt.CrossCursor)