_show_xlim_changes() - Code Metrics - Inspection of "Merge pull request #79 from andycasey/refactor" - andycasey/AnniesLasso - Measure and Improve Code Quality continuously with Scrutinizer

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Push — master ( b6035d...10c423 )

by Andy

created 2018-01-28 09:56 UTC

_show_xlim_changes() D

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cc	8
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dl	0
loc	38
rs	4



"""
Plot first-order element coefficients as a function of lambda.
"""


import matplotlib.pyplot as plt
#plt.rcParams["text.usetex"] = True
#plt.rcParams["text.latex.preamble"] = [r"\usepackage{amsmath}"]
import matplotlib.colors as cm
import numpy as np
import os
from scipy import optimize as op
from matplotlib.ticker import MaxNLocator

import colormaps as cmaps

import AnniesLasso as tc


def _show_xlim_changes(fig, diag=0.015, xtol=0):

    N = len(fig.axes)
    if 2 > N: return
    for i, ax in enumerate(fig.axes):

        if i > 0:
            # Put LHS break marks in.
            kwargs = dict(transform=ax.transAxes, color="k", clip_on=False)
            ax.plot((-diag, +diag), (  - diag,   + diag), **kwargs)
            ax.plot((-diag, +diag), (1 - diag, 1 + diag), **kwargs)

        if i != N - 1:
            # Put RHS break marks in.
            kwargs = dict(transform=ax.transAxes, color="k", clip_on=False)
            ax.plot((1 - diag, 1 + diag), (1 - diag, 1 + diag), **kwargs) 
            ax.plot((1 - diag, 1 + diag), (  - diag,   + diag), **kwargs)

        # Control spines depending on which axes it is
        if i == 0:
            ax.yaxis.tick_left() 
            ax.spines["right"].set_visible(False)
            ax.set_xlim(ax.get_xlim()[0], ax.get_xlim()[1] - xtol)

        elif i > 0 and i != N - 1:
            ax.set_xlim(ax.get_xlim()[0] + xtol, ax.get_xlim()[1] - xtol)
            ax.yaxis.set_tick_params(size=0)
            ax.tick_params(labelleft='off')
            ax.spines["left"].set_visible(False)
            ax.spines["right"].set_visible(False)

        else:
            ax.set_xlim(ax.get_xlim()[0] + xtol, ax.get_xlim()[1])
            ax.yaxis.tick_right()
            ax.tick_params(labelleft='off')
            ax.spines["left"].set_visible(False)

    return None



def plot_first_order_derivatives(model, label_names=None, scaled=True,
    show_clipped_region=False, colors=None, zorders=None,
    clip_less_than=None, label_wavelengths=None, latex_label_names=None,
    wavelength_regions=None, show_legend=True, **kwargs):

    if wavelength_regions is None:
        wavelength_regions = [(model.dispersion[0], model.dispersion[-1])]

    if label_names is None:
        label_names = model.vectorizer.label_names

    if latex_label_names is None:
        latex_label_names = {}

    fig, axes = plt.subplots(1, len(wavelength_regions), figsize=(15, 3.5))

    if len(label_names) > 1:
        #cmap = cm.LinearSegmentedColormap.from_list(
        #    "inferno", cmaps._inferno_data, len(label_names))
        cmap = plt.cm.get_cmap("Set1", len(label_names))
    else:
        cmap = lambda x: "k"

    if colors is not None:
        cmap = lambda x: colors[x % len(colors)]

    axes = np.array(axes).flatten()

    scales = []
    for i, label_name in enumerate(label_names):

        # First order derivatives are always indexed first.
        index = 1 + model.vectorizer.label_names.index(label_name)
        y = model.theta[:, index]
        #y = y
        if clip_less_than is not None:
            y[np.abs(y) < clip_less_than] = 0

        scale = np.nanmax(np.abs(y)) if scaled else 1.
        y = y / scale

        c = cmap(i)
        zorder = 1
        if zorders is not None: zorder = zorders[i]
        for ax in axes:
            ax.plot(model.dispersion, y, c=c, zorder=zorder,
                label=latex_label_names.get(label_name, label_name))

            if clip_less_than is not None and show_clipped_region:
                ax.axhspan(-clip_less_than/scale, +clip_less_than/scale,
                    xmin=-1, xmax=+2,
                    facecolor=c, edgecolor=c, zorder=-100, alpha=0.1)


    # Plot any wavelengths.
    if label_wavelengths is not None:
        label_yvalue = 1.0
        for label_name, wavelengths in label_wavelengths.items():
            try:
                color = cmap(label_names.index(label_name))
                label = None
            except (IndexError, ValueError):
                color = 'k'
                #for ax in axes:
                #    ax.plot([model.dispersion[0] - 1], [0], c=color, label=latex_label_names.get(label_name, label_name))

            for ax in axes:
                ax.plot(wavelengths, label_yvalue * np.ones_like(wavelengths),
                    "|", markersize=20, markeredgewidth=2, c=color)
    
    for ax, wavelength_region in zip(axes, wavelength_regions):
        ax.set_xlim(wavelength_region)
        if scaled:
            ax.set_ylim(-1.2, 1.2)
        
        if ax.is_first_col():
            if scaled:
                ax.set_ylabel(r"$\theta/{\max|\theta|}$")
            else:
                ax.set_ylabel(r"$\theta$")
        else:
            ax.set_yticklabels([])
    
        ax.xaxis.set_major_locator(MaxNLocator(4))

    xlabel = r"$\lambda$ $({\rm\AA})$"
    if len(wavelength_regions) == 1:
        ax.set_xlabel(xlabel)

    else:
        _show_xlim_changes(fig)
        
        ax = fig.add_axes([0, 0, 1, 1])
        ax.set_axis_off()
        ax.set_xlim(0, 1)
        ax.set_ylim(0, 1)
        ax.text(0.5, 0.05, xlabel, rotation='horizontal',
            horizontalalignment='center', verticalalignment='center')

    fig.tight_layout()

    if show_legend:
        axes[0].legend(loc="upper right", ncol=kwargs.get("legend_ncol", len(label_names) % 7), frameon=False)
    fig.subplots_adjust(wspace=0.01, bottom=0.20)

    return fig










if __name__ == "__main__":


    PATH, CATALOG, FILE_FORMAT = ("/Volumes/My Book/surveys/apogee/",
        "apogee-rg.fits", "apogee-rg-custom-normalization-{}.memmap")

    model = tc.load_model("gridsearch-20.0-3.0.model")
    model._dispersion = np.memmap(
        os.path.join(PATH, FILE_FORMAT).format("dispersion"),
        mode="c", dtype=float)



    fig = plot_first_order_derivatives(model,
        label_names=["AL_H", "S_H", "K_H"],
        clip_less_than=np.std(np.abs(model.theta[:, 6])),
        label_wavelengths={
            "AL_H": [16723.524113765838, 16767.938194147067],
            "K_H": [15172.521340566429],
            "Missing": [15235.7, 16755.1]
        },
        latex_label_names={
            "AL_H": r"$[\rm{Al}/\rm{H}]$",
            "K_H": r"$[\rm{K}/\rm{H}]$",
            "S_H": r"$[\rm{S}/\rm{H}]$",
            "Missing": "Missing/Unknown (Shetrone+ 2015)"
        },
        show_clipped_region=True,
        wavelength_regions=[
            (15152.465463818111, 15400),
            (16601, 16800),
        ])
    # Show first figure.
    fig.savefig("papers/sparse-first-order-coefficients.pdf", dpi=300)
    fig.savefig("papers/sparse-first-order-coefficients.png", dpi=300)

    # Now zoom in around those sections.

    colors = []
    cmap = plt.cm.get_cmap("Set1", 3)
    colors = [cmap(0)] + ["#CCCCCC"] * 11 + [cmap(1)] + ["#CCCCCC"] * 2

    fig = plot_first_order_derivatives(model,
        label_names=model.vectorizer.label_names[2:],
        clip_less_than=None, #np.std(np.abs(model.theta[:, 6])),
        scaled=True,
        show_clipped_region=False,
        colors=colors,
        zorders=[10] + [0] * 11 + [10] + [0] * 2,
        show_legend=False,
        latex_label_names={
            "AL_H": r"$[\rm{Al}/\rm{H}]$",
            "CA_H": r"$[\rm{Ca}/\rm{H}]$",
            "C_H": r"$[\rm{C}/\rm{H}]$",
            "FE_H": r"$[\rm{Fe}/\rm{H}]$",
            "K_H": r"$[\rm{K}/\rm{H}]$",
            "MG_H": r"$[\rm{Mg}/\rm{H}]$",
            "MN_H": r"$[\rm{Mn}/\rm{H}]$",
            "NA_H": r"$[\rm{Na}/\rm{H}]$",
            "NI_H": r"$[\rm{Ni}/\rm{H}]$",
            "N_H": r"$[\rm{N}/\rm{H}]$",
            "O_H": r"$[\rm{O}/\rm{H}]$",
            "SI_H": r"$[\rm{Si}/\rm{H}]$",
            "S_H": r"$[\rm{S}/\rm{H}]$",
            "TI_H": r"$[\rm{Ti}/\rm{H}]$",
            "V_H": r"$[\rm{V}/\rm{H}]$"
        },
        label_wavelengths={
            "Missing": [15235.7, 16755.1]
        },
        wavelength_regions=[
            (15235.6 - 10, 10 + 15235.6),
            (16755.1 - 10, 10 + 16755.1)
        ])

    for ax in fig.axes[:-1]:
        ax.set_xticklabels([r"${0:.0f}$".format(_) for _ in ax.get_xticks()])

    fig.savefig("papers/sparse-first-order-coefficients-zoom.pdf", dpi=300)
    fig.savefig("papers/sparse-first-order-coefficients-zoom.png", dpi=300)




1
2
3			"""
4			Plot first-order element coefficients as a function of lambda.
5			"""
6
7
8			import matplotlib.pyplot as plt
9			#plt.rcParams["text.usetex"] = True
10			#plt.rcParams["text.latex.preamble"] = [r"\usepackage{amsmath}"]
11			import matplotlib.colors as cm
12			import numpy as np
13			import os
14			from scipy import optimize as op
15			from matplotlib.ticker import MaxNLocator
16
17			import colormaps as cmaps
18
19			import AnniesLasso as tc
20
21
22			def _show_xlim_changes(fig, diag=0.015, xtol=0):
23
24			N = len(fig.axes)
25			if 2 > N: return
26			for i, ax in enumerate(fig.axes):
27
28			if i > 0:
29			# Put LHS break marks in.
30			kwargs = dict(transform=ax.transAxes, color="k", clip_on=False)
31			ax.plot((-diag, +diag), ( - diag, + diag), **kwargs)
32			ax.plot((-diag, +diag), (1 - diag, 1 + diag), **kwargs)
33
34			if i != N - 1:
35			# Put RHS break marks in.
36			kwargs = dict(transform=ax.transAxes, color="k", clip_on=False)
37			ax.plot((1 - diag, 1 + diag), (1 - diag, 1 + diag), **kwargs)
38			ax.plot((1 - diag, 1 + diag), ( - diag, + diag), **kwargs)
39
40			# Control spines depending on which axes it is
41			if i == 0:
42			ax.yaxis.tick_left()
43			ax.spines["right"].set_visible(False)
44			ax.set_xlim(ax.get_xlim()[0], ax.get_xlim()[1] - xtol)
45
46			elif i > 0 and i != N - 1:
47			ax.set_xlim(ax.get_xlim()[0] + xtol, ax.get_xlim()[1] - xtol)
48			ax.yaxis.set_tick_params(size=0)
49			ax.tick_params(labelleft='off')
50			ax.spines["left"].set_visible(False)
51			ax.spines["right"].set_visible(False)
52
53			else:
54			ax.set_xlim(ax.get_xlim()[0] + xtol, ax.get_xlim()[1])
55			ax.yaxis.tick_right()
56			ax.tick_params(labelleft='off')
57			ax.spines["left"].set_visible(False)
58
59			return None
60
61
62
63			def plot_first_order_derivatives(model, label_names=None, scaled=True,
64			show_clipped_region=False, colors=None, zorders=None,
65			clip_less_than=None, label_wavelengths=None, latex_label_names=None,
66			wavelength_regions=None, show_legend=True, **kwargs):
67
68			if wavelength_regions is None:
69			wavelength_regions = [(model.dispersion[0], model.dispersion[-1])]
70
71			if label_names is None:
72			label_names = model.vectorizer.label_names
73
74			if latex_label_names is None:
75			latex_label_names = {}
76
77			fig, axes = plt.subplots(1, len(wavelength_regions), figsize=(15, 3.5))
78
79			if len(label_names) > 1:
80			#cmap = cm.LinearSegmentedColormap.from_list(
81			# "inferno", cmaps._inferno_data, len(label_names))
82			cmap = plt.cm.get_cmap("Set1", len(label_names))
83			else:
84			cmap = lambda x: "k"
85
86			if colors is not None:
87			cmap = lambda x: colors[x % len(colors)]
88
89			axes = np.array(axes).flatten()
90
91			scales = []
92			for i, label_name in enumerate(label_names):
93
94			# First order derivatives are always indexed first.
95			index = 1 + model.vectorizer.label_names.index(label_name)
96			y = model.theta[:, index]
97			#y = y
98			if clip_less_than is not None:
99			y[np.abs(y) < clip_less_than] = 0
100
101			scale = np.nanmax(np.abs(y)) if scaled else 1.
102			y = y / scale
103
104			c = cmap(i)
105			zorder = 1
106			if zorders is not None: zorder = zorders[i]
107			for ax in axes:
108			ax.plot(model.dispersion, y, c=c, zorder=zorder,
109			label=latex_label_names.get(label_name, label_name))
110
111			if clip_less_than is not None and show_clipped_region:
112			ax.axhspan(-clip_less_than/scale, +clip_less_than/scale,
113			xmin=-1, xmax=+2,
114			facecolor=c, edgecolor=c, zorder=-100, alpha=0.1)
115
116
117			# Plot any wavelengths.
118			if label_wavelengths is not None:
119			label_yvalue = 1.0
120			for label_name, wavelengths in label_wavelengths.items():
121			try:
122			color = cmap(label_names.index(label_name))
123			label = None
124			except (IndexError, ValueError):
125			color = 'k'
126			#for ax in axes:
127			# ax.plot([model.dispersion[0] - 1], [0], c=color, label=latex_label_names.get(label_name, label_name))
128
129			for ax in axes:
130			ax.plot(wavelengths, label_yvalue * np.ones_like(wavelengths),
131			"\|", markersize=20, markeredgewidth=2, c=color)
132
133			for ax, wavelength_region in zip(axes, wavelength_regions):
134			ax.set_xlim(wavelength_region)
135			if scaled:
136			ax.set_ylim(-1.2, 1.2)
137
138			if ax.is_first_col():
139			if scaled:
140			ax.set_ylabel(r"$\theta/{\max\|\theta\|}$")
141			else:
142			ax.set_ylabel(r"$\theta$")
143			else:
144			ax.set_yticklabels([])
145
146			ax.xaxis.set_major_locator(MaxNLocator(4))
147
148			xlabel = r"$\lambda$ $({\rm\AA})$"
149			if len(wavelength_regions) == 1:
150			ax.set_xlabel(xlabel)
151
152			else:
153			_show_xlim_changes(fig)
154
155			ax = fig.add_axes([0, 0, 1, 1])
156			ax.set_axis_off()
157			ax.set_xlim(0, 1)
158			ax.set_ylim(0, 1)
159			ax.text(0.5, 0.05, xlabel, rotation='horizontal',
160			horizontalalignment='center', verticalalignment='center')
161
162			fig.tight_layout()
163
164			if show_legend:
165			axes[0].legend(loc="upper right", ncol=kwargs.get("legend_ncol", len(label_names) % 7), frameon=False)
166			fig.subplots_adjust(wspace=0.01, bottom=0.20)
167
168			return fig
169
170
171
172
173
174
175
176
177
178
179			if __name__ == "__main__":
180
181
182			PATH, CATALOG, FILE_FORMAT = ("/Volumes/My Book/surveys/apogee/",
183			"apogee-rg.fits", "apogee-rg-custom-normalization-{}.memmap")
184
185			model = tc.load_model("gridsearch-20.0-3.0.model")
186			model._dispersion = np.memmap(
187			os.path.join(PATH, FILE_FORMAT).format("dispersion"),
188			mode="c", dtype=float)
189
190
191
192			fig = plot_first_order_derivatives(model,
193			label_names=["AL_H", "S_H", "K_H"],
194			clip_less_than=np.std(np.abs(model.theta[:, 6])),
195			label_wavelengths={
196			"AL_H": [16723.524113765838, 16767.938194147067],
197			"K_H": [15172.521340566429],
198			"Missing": [15235.7, 16755.1]
199			},
200			latex_label_names={
201			"AL_H": r"$[\rm{Al}/\rm{H}]$",
202			"K_H": r"$[\rm{K}/\rm{H}]$",
203			"S_H": r"$[\rm{S}/\rm{H}]$",
204			"Missing": "Missing/Unknown (Shetrone+ 2015)"
205			},
206			show_clipped_region=True,
207			wavelength_regions=[
208			(15152.465463818111, 15400),
209			(16601, 16800),
210			])
211			# Show first figure.
212			fig.savefig("papers/sparse-first-order-coefficients.pdf", dpi=300)
213			fig.savefig("papers/sparse-first-order-coefficients.png", dpi=300)
214
215			# Now zoom in around those sections.
216
217			colors = []
218			cmap = plt.cm.get_cmap("Set1", 3)
219			colors = [cmap(0)] + ["#CCCCCC"] * 11 + [cmap(1)] + ["#CCCCCC"] * 2
220
221			fig = plot_first_order_derivatives(model,
222			label_names=model.vectorizer.label_names[2:],
223			clip_less_than=None, #np.std(np.abs(model.theta[:, 6])),
224			scaled=True,
225			show_clipped_region=False,
226			colors=colors,
227			zorders=[10] + [0] * 11 + [10] + [0] * 2,
228			show_legend=False,
229			latex_label_names={
230			"AL_H": r"$[\rm{Al}/\rm{H}]$",
231			"CA_H": r"$[\rm{Ca}/\rm{H}]$",
232			"C_H": r"$[\rm{C}/\rm{H}]$",
233			"FE_H": r"$[\rm{Fe}/\rm{H}]$",
234			"K_H": r"$[\rm{K}/\rm{H}]$",
235			"MG_H": r"$[\rm{Mg}/\rm{H}]$",
236			"MN_H": r"$[\rm{Mn}/\rm{H}]$",
237			"NA_H": r"$[\rm{Na}/\rm{H}]$",
238			"NI_H": r"$[\rm{Ni}/\rm{H}]$",
239			"N_H": r"$[\rm{N}/\rm{H}]$",
240			"O_H": r"$[\rm{O}/\rm{H}]$",
241			"SI_H": r"$[\rm{Si}/\rm{H}]$",
242			"S_H": r"$[\rm{S}/\rm{H}]$",
243			"TI_H": r"$[\rm{Ti}/\rm{H}]$",
244			"V_H": r"$[\rm{V}/\rm{H}]$"
245			},
246			label_wavelengths={
247			"Missing": [15235.7, 16755.1]
248			},
249			wavelength_regions=[
250			(15235.6 - 10, 10 + 15235.6),
251			(16755.1 - 10, 10 + 16755.1)
252			])
253
254			for ax in fig.axes[:-1]:
255			ax.set_xticklabels([r"${0:.0f}$".format(_) for _ in ax.get_xticks()])
256
257			fig.savefig("papers/sparse-first-order-coefficients-zoom.pdf", dpi=300)
258			fig.savefig("papers/sparse-first-order-coefficients-zoom.png", dpi=300)
259
260
261

andycasey / AnniesLasso

Push — master ( b6035d...10c423 )

_show_xlim_changes() D

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