diff --git a/pylk/pylk/colormodes.py b/pylk/pylk/colormodes.py
new file mode 100644
index 0000000000000000000000000000000000000000..1e64bed7e4e859c29d4555895fb8f62088bf5129
--- /dev/null
+++ b/pylk/pylk/colormodes.py
@@ -0,0 +1,419 @@
+""" Color modes for graphed pintk TOAs. """
+import numpy as np
+import matplotlib
+import matplotlib.colors
+
+
+# subset of other colors to allow users to distinguish between them
+named_colors = [
+ "xkcd:red",
+ "xkcd:green",
+ "xkcd:cyan",
+ "xkcd:blue",
+ "xkcd:burnt orange",
+ "xkcd:brown",
+ "xkcd:indigo",
+ "xkcd:purple",
+ "xkcd:dark blue",
+ "xkcd:light green",
+ "xkcd:dark green",
+ "xkcd:light blue",
+ "xkcd:dark red",
+ "xkcd:magenta",
+ "xkcd:black",
+ "xkcd:grey",
+ "xkcd:light grey",
+ "xkcd:yellow",
+ "xkcd:orange",
+]
+
+
+class ColorMode:
+ """Base Class for color modes."""
+
+ def __init__(self, application):
+ self.application = application # PLKWidget for pintk
+
+ def displayInfo(self):
+ raise NotImplementedError
+
+ def plotColorMode(self):
+ raise NotImplementedError
+
+
+class DefaultMode(ColorMode):
+ """
+ A class to manage the Default color mode, where TOAs are colored
+ blue as a default and red if jumped.
+ """
+
+ def __init__(self, application):
+ super().__init__(application)
+ self.mode_name = "default"
+
+ def displayInfo(self):
+ print(
+ '"Default" mode selected\n'
+ #+ " Blue = default color\n"
+ #+ " Orange = selected TOAs\n"
+ #+ " Red = jumped TOAs\n"
+ + " Cyan = default color\n"
+ + " Orange = selected TOAs\n"
+ + " Magenta = jumped TOAs\n"
+ )
+
+ def plotColorMode(self):
+ """
+ Plots application's residuals in proper color scheme.
+ """
+ if self.application.yerrs is None:
+ self.application.plkAxes.scatter(
+ self.application.xvals[~self.application.selected],
+ self.application.yvals[~self.application.selected],
+ marker=".",
+ color="xkcd:cyan",
+ )
+ self.application.plkAxes.scatter(
+ self.application.xvals[self.application.jumped],
+ self.application.yvals[self.application.jumped],
+ marker=".",
+ color="xkcd:magenta",
+ )
+ self.application.plkAxes.scatter(
+ self.application.xvals[self.application.selected],
+ self.application.yvals[self.application.selected],
+ marker=".",
+ color="xkcd:burnt orange",
+ )
+ else:
+ self.application.plotErrorbar(~self.application.selected, color="xkcd:cyan")
+ self.application.plotErrorbar(self.application.jumped, color="xkcd:burnt orange")
+ self.application.plotErrorbar(self.application.selected, color="xkcd:magenta")
+
+
+class FreqMode(ColorMode):
+ """
+ A class to manage the Frequency color mode, where TOAs are colored
+ according to their frequency.
+ """
+
+ def __init__(self, application):
+ super().__init__(application)
+ self.mode_name = "freq"
+
+ def displayInfo(self):
+ print(
+ '"Frequency" mode selected\n'
+ + " Dark Red < 300 MHz\n"
+ + " Red = 300-400 MHz\n"
+ + " Orange = 400-500 MHz\n"
+ + " Yellow = 500-700 MHz\n"
+ + " Green = 700-1000 MHz\n"
+ + " Blue = 1000-1800 MHz\n"
+ + " Indigo = 1800-3000 MHz\n"
+ + " Black = 3000-8000 MHz\n"
+ + " Grey > 8000 MHz\n"
+ + " Brown is for selected TOAs\n"
+ )
+
+ def plotColorMode(self):
+ """
+ Plots application's residuals in proper color scheme.
+ """
+
+ colorGroups = [
+ "xkcd:dark red", # dark red
+ "xkcd:red", # red
+ "xkcd:orange", # orange
+ "xkcd:yellow", # yellow
+ "xkcd:green", # green
+ "xkcd:blue", # blue
+ "xkcd:indigo", # indigo
+ "xkcd:black", # black
+ "xkcd:grey", # grey
+ ]
+ highfreqs = [300.0, 400.0, 500.0, 700.0, 1000.0, 1800.0, 3000.0, 8000.0]
+
+ freqGroups = []
+ for ii, highfreq in enumerate(highfreqs):
+ if ii == 0:
+ freqGroups.append(
+ self.application.psr.all_toas.get_freqs().value < highfreq
+ )
+ else:
+ freqGroups.append(
+ (self.application.psr.all_toas.get_freqs().value < highfreq)
+ & (
+ self.application.psr.all_toas.get_freqs().value
+ >= highfreqs[ii - 1]
+ )
+ )
+ freqGroups.append(
+ self.application.psr.all_toas.get_freqs().value >= highfreqs[-1]
+ )
+
+ for index in range(len(freqGroups)):
+ if self.application.yerrs is None:
+ self.application.plkAxes.scatter(
+ self.application.xvals[freqGroups[index]],
+ self.application.yvals[freqGroups[index]],
+ marker=".",
+ color=colorGroups[index],
+ )
+ else:
+ self.application.plotErrorbar(
+ freqGroups[index], color=colorGroups[index]
+ )
+ # The following is for selected TOAs
+ if self.application.yerrs is None:
+ self.application.plkAxes.scatter(
+ self.application.xvals[self.application.selected],
+ self.application.yvals[self.application.selected],
+ marker=".",
+ color="#362511", # brown
+ )
+ else:
+ self.application.plotErrorbar(self.application.selected, color="#362511")
+
+
+class NameMode(ColorMode):
+ """
+ A class to manage the Frequency color mode, where TOAs are colored
+ according to their names in the TOA lines.
+ """
+
+ def __init__(self, application):
+ super().__init__(application)
+ self.mode_name = "name"
+
+ def displayInfo(self):
+ print('"Name" mode selected\n' + " Orange = selected TOAs\n")
+
+ def plotColorMode(self):
+ """
+ Plots application's residuals in proper color scheme.
+ """
+
+ all_names = np.array(
+ [f["name"] for f in self.application.psr.all_toas.get_flags()]
+ )
+ single_names = list(set(all_names))
+ N = len(single_names)
+ cmap = matplotlib.cm.get_cmap("brg")
+ colorGroups = [matplotlib.colors.rgb2hex(cmap(v)) for v in np.linspace(0, 1, N)]
+ colorGroups += ["orange"]
+
+ freqGroups = []
+ index = 0
+ for name in single_names:
+ index += 1
+ freqGroups.append(all_names == name)
+ index += 1
+
+ for index in range(N):
+ if self.application.yerrs is None:
+ self.application.plkAxes.scatter(
+ self.application.xvals[freqGroups[index]],
+ self.application.yvals[freqGroups[index]],
+ marker=".",
+ color=colorGroups[index],
+ )
+ else:
+ self.application.plotErrorbar(
+ freqGroups[index], color=colorGroups[index]
+ )
+
+ if self.application.yerrs is None:
+ self.application.plkAxes.scatter(
+ self.application.xvals[self.application.selected],
+ self.application.yvals[self.application.selected],
+ marker=".",
+ color=colorGroups[N],
+ )
+ else:
+ self.application.plotErrorbar(
+ self.application.selected, color=colorGroups[N]
+ )
+
+
+class ObsMode(ColorMode):
+ """
+ A class to manage the Observatory color mode, where TOAs are colored
+ according to their observatory.
+ """
+
+ def __init__(self, application):
+ super().__init__(application)
+ self.mode_name = "obs"
+
+ def get_obs_mapping(self):
+ "This maps the obs names in the TOAs to our local subset"
+ tmp_obs = self.application.psr.all_toas.observatories
+ mapping = {}
+ for oo in tmp_obs:
+ if "stl" in oo:
+ mapping[oo] = "space"
+ elif oo.startswith("gb"):
+ mapping[oo] = "gb"
+ elif oo.startswith("jb"):
+ mapping[oo] = "jodrell"
+ elif "ncy" in oo:
+ mapping[oo] = "nancay"
+ else:
+ mapping[oo] = oo if oo in self.obs_colors else "other"
+ return mapping
+
+ obs_colors = {
+ "parkes": "xkcd:red",
+ "gb": "xkcd:green", # this is any green bank obs
+ "jodrell": "xkcd:cyan",
+ "arecibo": "xkcd:blue",
+ "chime": "xkcd:burnt orange",
+ "gmrt": "xkcd:brown",
+ "vla": "xkcd:indigo",
+ "effelsberg": "xkcd:purple",
+ "fast": "xkcd:dark blue",
+ "nancay": "xkcd:light green",
+ "srt": "xkcd:dark green",
+ "wsrt": "xkcd:light blue",
+ "lofar": "xkcd:dark red",
+ "lwa": "xkcd:dark red",
+ "mwa": "xkcd:dark red",
+ "meerkat": "xkcd:magenta",
+ "barycenter": "xkcd:black",
+ "geocenter": "xkcd:grey",
+ "space": "xkcd:light grey",
+ "other": "xkcd:yellow",
+ }
+ selected_color = "orange"
+
+ obs_text = {}
+ for obs in obs_colors:
+ # try to get all of the capitalization special cases right
+ if obs in ["parkes", "jodrell", "arecibo", "nancay", "effelsberg"]:
+ obs_name = obs.capitalize()
+ elif obs in ["barycenter", "geocenter", "space", "other"]:
+ obs_name = obs
+ elif obs in ["gb"]:
+ obs_name = "Green Bank"
+ elif obs in ["meerkat"]:
+ obs_name = "MeerKAT"
+ else:
+ obs_name = obs.upper()
+ obs_text[
+ obs
+ ] = f" {obs_colors[obs].replace('xkcd:','').capitalize()} = {obs_name}"
+
+ def displayInfo(self):
+ outstr = '"Observatory" mode selected\n'
+ for obs in self.get_obs_mapping().values():
+ outstr += self.obs_text[obs].replace("xkcd", "") + "\n"
+ outstr += f" {self.selected_color.capitalize()} = selected\n"
+ print(outstr)
+
+ def plotColorMode(self):
+ """
+ Plots application's residuals in proper color scheme.
+ """
+ obsmap = self.get_obs_mapping()
+ alltoas = self.application.psr.all_toas
+ for obs, ourobs in obsmap.items():
+ # group toa indices by observatory
+ toas = alltoas.get_obss() == obs
+ color = self.obs_colors[ourobs]
+ if self.application.yerrs is None:
+ self.application.plkAxes.scatter(
+ self.application.xvals[toas],
+ self.application.yvals[toas],
+ marker=".",
+ color=color,
+ )
+ else:
+ self.application.plotErrorbar(toas, color=color)
+ # Now handle the selected TOAs
+ if self.application.yerrs is None:
+ self.application.plkAxes.scatter(
+ self.application.xvals[self.application.selected],
+ self.application.yvals[self.application.selected],
+ marker=".",
+ color=self.selected_color,
+ )
+ else:
+ self.application.plotErrorbar(
+ self.application.selected, color=self.selected_color
+ )
+
+
+class JumpMode(ColorMode):
+ """Mode to color points according to jump"""
+
+ def __init__(self, application):
+ super().__init__(application)
+ self.mode_name = "jump"
+
+ def get_jumps(self):
+ """Return the jump objects for the `psr` model or an empty list
+
+ Returns
+ -------
+ list :
+ List of jump objects
+ """
+ if self.application.psr.fitted:
+ model = self.application.psr.postfit_model
+ else:
+ model = self.application.psr.prefit_model
+ if "PhaseJump" not in model.components:
+ return []
+ return model.get_jump_param_objects()
+
+ jump_colors = named_colors
+ selected_color = "xkcd:orange"
+
+ def displayInfo(self):
+ outstr = '"Jump" mode selected\n'
+ for jumpnum, jump in enumerate(self.get_jumps()):
+ # only use the number of colors - 1 to preserve orange for selected
+ color_number = jumpnum % (len(self.jump_colors) - 1)
+ color_name = self.jump_colors[color_number]
+ outstr += f" {color_name.replace('xkcd:','').capitalize()} = "
+ outstr += f"{jump.name}"
+ if jump.key is not None:
+ outstr += f" {jump.key}"
+ if jump.key_value is not None:
+ outstr += " " + " ".join(jump.key_value)
+ outstr += "\n"
+ outstr += (
+ f" {self.selected_color.replace('xkcd:','').capitalize()} = selected\n"
+ )
+ print(outstr)
+
+ def plotColorMode(self):
+ """Plot the points with the desired coloring"""
+ alltoas = self.application.psr.all_toas
+ for jumpnum, jump in enumerate(self.get_jumps()):
+ color_number = jumpnum % (len(self.jump_colors) - 1)
+ color_name = self.jump_colors[color_number]
+ toas = jump.select_toa_mask(alltoas)
+ # group toa indices by jump
+ if self.application.yerrs is None:
+ self.application.plkAxes.scatter(
+ self.application.xvals[toas],
+ self.application.yvals[toas],
+ marker=".",
+ color=color_name,
+ )
+ else:
+ self.application.plotErrorbar(toas, color=color_name)
+ # Now handle the selected TOAs
+ if self.application.yerrs is None:
+ self.application.plkAxes.scatter(
+ self.application.xvals[self.application.selected],
+ self.application.yvals[self.application.selected],
+ marker=".",
+ color=self.selected_color,
+ )
+ else:
+ self.application.plotErrorbar(
+ self.application.selected, color=self.selected_color
+ )
diff --git a/pylk/pylk/constants.py b/pylk/pylk/constants.py
index 4ee4a204637f3c75a77d0c8c003512ec3e12ebe3..cbfd41ca49338a05dc1ef13c798bcbd5901285a4 100644
--- a/pylk/pylk/constants.py
+++ b/pylk/pylk/constants.py
@@ -10,16 +10,17 @@ import matplotlib as mpl
PylkBanner = """
+----------------------------------------------+
| PINT |
- | ==== ,~~~~. |
- | Modern Pulsar Timing i====i_ |
- | |cccc|_) |
- | Brought to you by the |cccc| |
- | NANOGrav collaboration `-==-' |
+ | ==== ,~~~~. |
+ | Modern Pulsar Timing i====i_ |
+ | |cccc|_) |
+ | Brought to you by the |cccc| |
+ | NANOGrav collaboration `-==-' |
| |
+----------------------------------------------+
"""
+
#winsize_with_jupyter = (1350, 550)
#winsize_without_jupyter = (650, 550)
winsize_with_jupyter = (1400, 700)
@@ -58,11 +59,14 @@ mpl_rcParams_black = dict({
'axes.facecolor': 'black',
'axes.edgecolor': 'white',
'axes.labelcolor': 'white',
- 'axes.prop_cycle': mpl.cycler(color=['y', 'm', 'c', 'r', 'g', 'b', 'w']),
+ #'axes.prop_cycle': mpl.cycler(color=['y', 'm', 'c', 'r', 'g', 'b', 'w']),
+ 'axes.prop_cycle': mpl.cycler(color=['#8dd3c7', '#feffb3', '#bfbbd9', '#fa8174', '#81b1d2', '#fdb462', '#b3de69', '#bc82bd', '#ccebc4', '#ffed6f']),
'xtick.color': 'white',
'ytick.color': 'white',
'grid.color': 'grey',
'grid.linestyle': 'dashed',
+ 'grid.linewidth': '0.5',
+ 'grid.alpha': '0.5',
'figure.facecolor': 'black',
'figure.edgecolor': 'black',
'savefig.facecolor': 'black',
diff --git a/pylk/pylk/plk.py b/pylk/pylk/plk.py
index 5d8e1748e9e3c6715fccd97cedbd13d6b19a197b..b31ab800fe3b2c7247c6bc3a6adf74858a264779 100644
--- a/pylk/pylk/plk.py
+++ b/pylk/pylk/plk.py
@@ -77,7 +77,8 @@ import astropy.units as u
import numpy as np
import pint.pintk.pulsar as pulsar
-import pint.pintk.colormodes as cm
+from pylk import colormodes as cm
+#import pint.pintk.colormodes as cm
#from pylk import pulsar # Not used anymore
from pylk import constants
@@ -422,6 +423,7 @@ class PlkFitboxesWidget(QWidget):
self.boxChecked(parchanged, bool(w.widget().checkState()))
print("{0} set to {1}".format(parchanged, bool(w.widget().checkState())))
+
class PlkRandomModelSelect(QFrame):
"""
Allows one to select whether to fit with random models or not
@@ -563,7 +565,7 @@ class PlkColorModeBoxes(QWidget):
self.group.addButton(radiobutton)
self.layout.addWidget(radiobutton)
self.radiobuttons.append(radiobutton)
-
+
if mode.mode_name == "default":
# default mode should be selected at start-up
radiobutton.setChecked(True)
@@ -1102,7 +1104,8 @@ class PlkWidget(QWidget):
#rcP['savefig.facecolor'] = rgbcolor
#rcP['savefig.edgecolor'] = rgbcolor
- for key, value in rcP.items():
+ #for key, value in rcP.items():
+ for key, value in constants.mpl_rcParams_black.items():
mpl.rcParams[key] = value
else:
for key, value in constants.mpl_rcParams_black.items():
@@ -1538,7 +1541,8 @@ class PlkWidget(QWidget):
mjd = m.conjunction(tt)
pb = m.pb()[0].to_value("day")
phs = (mjd - tt) / pb
- self.plkAxes.plot([phs, phs], [ymin, ymax], "k-")
+ # TODO: Color
+ self.plkAxes.plot([phs, phs], [ymin, ymax], "w-")
else:
self.plkAxes.set_ylabel(plotlabels[self.yid])
@@ -1565,8 +1569,9 @@ class PlkWidget(QWidget):
sort_inds = np.argsort(f_toas_plot)
f_toas_plot = f_toas_plot[sort_inds]
for i in range(len(rs)):
+ # TODO: Color
self.plkAxes.plot(
- f_toas_plot, rs[i][sort_inds] * scale, "-k", alpha=0.3
+ f_toas_plot, rs[i][sort_inds] * scale, "-w", alpha=0.3
)
def determine_yaxis_units(self, miny, maxy):