Example #1
0
def plot(LSM, fileName=None, labelBy=None):
    """
    Shows a simple plot of the sky model.

    The circles in the plot are scaled with flux. If the sky model is grouped
    into patches, sources are colored by patch and the patch positions are
    indicated with stars.

    Parameters
    ----------
    LSM : SkyModel object
        Input sky model
    fileName : str, optional
        If given, the plot is saved to a file instead of displayed
    labelBy : str, optional
        One of 'source' or 'patch': label points using source names ('source') or
        patch names ('patch')

    Examples:
    ---------
    Plot and display to the screen::

        >>> LSM = lsmtool.load('sky.model')
        >>> plot(LSM)

    Plot and save to a PDF file::

        >>> plot(LSM, 'sky_plot.pdf')

    """
    try:
        import os
        if 'DISPLAY' not in os.environ:
            import matplotlib
            if matplotlib.get_backend() is not 'Agg':
                matplotlib.use("Agg")
        import matplotlib.pyplot as plt
        from matplotlib.ticker import FuncFormatter
    except Exception as e:
        raise ImportError('PyPlot could not be imported. Plotting is not '
                          'available: {0}'.format(e.message))
    try:
        try:
            from astropy.visualization.wcsaxes import WCSAxes
            hasWCSaxes = True
        except:
            from wcsaxes import WCSAxes
            hasWCSaxes = True
    except:
        hasWCSaxes = False
    import numpy as np
    from ..operations_lib import radec2xy, makeWCS
    global midRA, midDec, ymin, xmin

    if len(LSM) == 0:
        log.error('Sky model is empty.')
        return

    fig = plt.figure(1, figsize=(7.66, 7))
    plt.clf()
    x, y, midRA, midDec = LSM._getXY()
    if hasWCSaxes:
        wcs = makeWCS(midRA, midDec)
        ax = WCSAxes(fig, [0.16, 0.1, 0.8, 0.8], wcs=wcs)
        fig.add_axes(ax)
    else:
        ax = plt.gca()
    if LSM.hasPatches:
        nsrc = len(LSM.getPatchNames())
    else:
        nsrc = len(LSM)
    sm = plt.cm.ScalarMappable(cmap=plt.cm.Set3,
                               norm=plt.Normalize(vmin=0, vmax=nsrc))
    sm._A = []

    # Set symbol sizes by flux, making sure no symbol is smaller than 50 or
    # larger than 1000
    s = []
    fluxes = LSM.getColValues('I')
    if len(fluxes[fluxes > 0.0]) == 0:
        minflux = 0.0
    else:
        minflux = np.min(fluxes[fluxes > 0.0])
    for flux in LSM.getColValues('I'):
        if flux > 0.0:
            s.append(min(1000.0,
                         (1.0 + 2.0 * np.log10(flux / minflux)) * 50.0))
        else:
            s.append(50.0)

    # Color sources by patch if grouped
    c = [0] * len(LSM)
    cp = []
    if LSM.hasPatches:
        for p, patchName in enumerate(LSM.getPatchNames()):
            indices = LSM.getRowIndex(patchName)
            cp.append(sm.to_rgba(p))
            for ind in indices:
                c[ind] = sm.to_rgba(p)
    else:
        c = [sm.to_rgba(0)] * nsrc

    # Plot sources
    if hasWCSaxes:
        RA = LSM.getColValues('Ra')
        Dec = LSM.getColValues('Dec')
        ax.set_xlim(np.min(x) - 20, np.max(x) + 20)
        ax.set_ylim(np.min(y) - 20, np.max(y) + 20)
    plt.scatter(x, y, s=s, c=c)

    if LSM.hasPatches:
        RAp, Decp = LSM.getPatchPositions(asArray=True)
        goodInd = np.where((RAp != 0.0) & (Decp != 0.0))
        if len(goodInd[0]) < len(RAp):
            log.info('Some patch positions are unset. Run setPatchPositions() '
                     'before plotting to see patch positions and patch names.')
        xp, yp = radec2xy(RAp[goodInd], Decp[goodInd], midRA, midDec)
        plt.scatter(xp, yp, s=100, c=cp, marker='*')

    # Set axis labels, etc.
    if hasWCSaxes:
        RAAxis = ax.coords['ra']
        RAAxis.set_axislabel('RA', minpad=0.75)
        RAAxis.set_major_formatter('hh:mm:ss')
        DecAxis = ax.coords['dec']
        DecAxis.set_axislabel('Dec', minpad=0.75)
        DecAxis.set_major_formatter('dd:mm:ss')
        ax.coords.grid(color='black', alpha=0.5, linestyle='solid')
    else:
        plt.xlabel("RA (arb. units)")
        plt.ylabel("Dec (arb. units)")

    if labelBy is not None:
        if labelBy.lower() == 'source':
            labels = LSM.getColValues('name')
            xls = x
            yls = y
        elif labelBy.lower() == 'patch':
            if LSM.hasPatches:
                labels = LSM.getPatchNames()
                xls = xp
                yls = yp
            else:
                labels = LSM.getColValues('name')
                xls = x
                yls = y
        else:
            raise ValueError(
                "The lableBy parameter must be one of 'source' or "
                "'patch'.")
        for label, xl, yl in zip(labels, xls, yls):
            plt.annotate(label,
                         xy=(xl, yl),
                         xytext=(-2, 2),
                         textcoords='offset points',
                         ha='right',
                         va='bottom')

    # Define coodinate formater to show RA and Dec under mouse pointer
    RAformatter = FuncFormatter(RAtickformatter)
    ax.format_coord = formatCoord

    if fileName is not None:
        plt.savefig(fileName)
    else:
        plt.show()
    plt.close(fig)
Example #2
0
def plot_state(directions_list, trim_names=True):
    """
    Plots the facets of a run
    """
    global midRA, midDec, fig, at, selected_direction, choose_from_list
    selected_direction = None
    choose_from_list = False

    # Set up coordinate system and figure
    points, midRA, midDec = factor.directions.getxy(directions_list)
    fig = plt.figure(1, figsize=(10,9))
    if hasWCSaxes:
        wcs = factor.directions.makeWCS(midRA, midDec)
        ax = WCSAxes(fig, [0.16, 0.1, 0.8, 0.8], wcs=wcs)
        fig.add_axes(ax)
    else:
        ax = plt.gca()

    field_x = min(points[0])
    field_y = max(points[1])
    adjust_xy = True
    while adjust_xy:
        adjust_xy = False
        for xy in points:
            dist = np.sqrt( (xy[0] - field_x)**2 + (xy[1] - field_y)**2 )
            if dist < 10.0:
                field_x -= 1
                field_y += 1
                adjust_xy = True
                break
    field_ra, field_dec = factor.directions.xy2radec([field_x], [field_y],
        refRA=midRA, refDec=midDec)
    field = Direction('field', field_ra[0], field_dec[0],
        factor_working_dir=directions_list[0].working_dir)
    directions_list.append(field)

    ax.set_title('Overview of Factor run in\n{}'.format(directions_list[0].working_dir))

    # Plot facets
    markers = []
    for direction in directions_list:
        if direction.name != 'field':
            vertices = read_vertices(direction.vertices_file)
            RAverts = vertices[0]
            Decverts = vertices[1]
            xverts, yverts = factor.directions.radec2xy(RAverts, Decverts,
                refRA=midRA, refDec=midDec)
            xyverts = [np.array([xp, yp]) for xp, yp in zip(xverts, yverts)]
            mpl_poly = Polygon(np.array(xyverts), edgecolor='#a9a9a9', facecolor='#F2F2F2',
                clip_box=ax.bbox, picker=3.0, linewidth=2)
        else:
            xverts = [field_x]
            yverts = [field_y]
            mpl_poly = Circle((field_x, field_y), radius=5.0, edgecolor='#a9a9a9', facecolor='#F2F2F2',
                clip_box=ax.bbox, picker=3.0, linewidth=2)
        mpl_poly.facet_name = direction.name
        mpl_poly.completed_ops = get_completed_ops(direction)
        mpl_poly.started_ops = get_started_ops(direction)
        mpl_poly.current_op = get_current_op(direction)
        set_patch_color(mpl_poly, direction)
        ax.add_patch(mpl_poly)

        # Add facet names
        if direction.name != 'field':
            poly_tuple = tuple([(xp, yp) for xp, yp in zip(xverts, yverts)])
            xmid = SPolygon(poly_tuple).centroid.x
            ymid = SPolygon(poly_tuple).centroid.y
        else:
            xmid = field_x
            ymid = field_y
        if trim_names:
            name = direction.name.split('_')[-1]
        else:
            name = direction.name
        marker = ax.text(xmid, ymid, name, color='k', clip_on=True,
            clip_box=ax.bbox, ha='center', va='bottom')
        marker.set_zorder(1001)
        markers.append(marker)

    # Add info box
    at = AnchoredText("Selected direction: None", prop=dict(size=12), frameon=True,
        loc=3)
    at.patch.set_boxstyle("round,pad=0.,rounding_size=0.2")
    at.set_zorder(1002)
    ax.add_artist(at)

    ax.relim()
    ax.autoscale()
    ax.set_aspect('equal')

    if hasWCSaxes:
        RAAxis = ax.coords['ra']
        RAAxis.set_axislabel('RA', minpad=0.75)
        RAAxis.set_major_formatter('hh:mm:ss')
        DecAxis = ax.coords['dec']
        DecAxis.set_axislabel('Dec', minpad=0.75)
        DecAxis.set_major_formatter('dd:mm:ss')
        ax.coords.grid(color='black', alpha=0.5, linestyle='solid')
    else:
        plt.xlabel("RA (arb. units)")
        plt.ylabel("Dec (arb. units)")

    # Define coodinate formater to show RA and Dec under mouse pointer
    ax.format_coord = formatCoord

    # Show legend
    not_processed_patch = plt.Rectangle((0, 0), 1, 1, edgecolor='#a9a9a9',
        facecolor='#F2F2F2', linewidth=2)
    processing_patch = plt.Rectangle((0, 0), 1, 1, edgecolor='#a9a9a9',
        facecolor='#F2F5A9', linewidth=2)
    selfcal_ok_patch = plt.Rectangle((0, 0), 1, 1, edgecolor='#a9a9a9',
        facecolor='#A9F5A9', linewidth=2)
    selfcal_not_ok_patch = plt.Rectangle((0, 0), 1, 1, edgecolor='#a9a9a9',
        facecolor='#A4A4A4', linewidth=2)
    processing_error = plt.Rectangle((0, 0), 1, 1, edgecolor='#a9a9a9',
        facecolor='#F5A9A9', linewidth=2)
    patch_list=[not_processed_patch, processing_patch, processing_error, selfcal_not_ok_patch, selfcal_ok_patch]
    label_list=['Unprocessed', 'Processing', 'Pipeline Error', 'Selfcal Failed', 'Selfcal OK']
    for i in range(options['reimages']):
        label_list.append('Image '+str(i+1))
        color=(0.66/(i+2)**0.5, 0.96/(i+2)**0.5, 0.66/(i+2)**0.5, 1.0)
        reimage_patch=plt.Rectangle((0, 0), 1, 1, edgecolor='#a9a9a9',
            facecolor=color, linewidth=2)
        patch_list.append(reimage_patch)
    l = ax.legend(patch_list, label_list, loc="upper right")
    l.set_zorder(1002)

    # Add check for mouse clicks and key presses
    fig.canvas.mpl_connect('pick_event', on_pick)
    fig.canvas.mpl_connect('key_press_event', on_press)

    # Add timer to update the plot every 60 seconds
    timer = fig.canvas.new_timer(interval=60000)
    timer.add_callback(update_plot)
    timer.start()

    # Show plot
    plt.show()
    plt.close(fig)

    # Clean up any temp casacore images
    if not hasaplpy:
        if os.path.exists('/tmp/tempimage'):
            try:
                shutil.rmtree('/tmp/tempimage')
            except OSError:
                pass
Example #3
0
def plot_state(directions_list, trim_names=True):
    """
    Plots the facets of a run
    """
    global midRA, midDec, fig, at, selected_direction, choose_from_list
    selected_direction = None
    choose_from_list = False

    # Set up coordinate system and figure
    points, midRA, midDec = factor.directions.getxy(directions_list)
    fig = plt.figure(1, figsize=(10, 9))
    if hasWCSaxes:
        wcs = factor.directions.makeWCS(midRA, midDec)
        ax = WCSAxes(fig, [0.16, 0.1, 0.8, 0.8], wcs=wcs)
        fig.add_axes(ax)
    else:
        ax = plt.gca()

    field_x = min(points[0])
    field_y = max(points[1])
    adjust_xy = True
    while adjust_xy:
        adjust_xy = False
        for xy in points:
            dist = np.sqrt((xy[0] - field_x)**2 + (xy[1] - field_y)**2)
            if dist < 10.0:
                field_x -= 1
                field_y += 1
                adjust_xy = True
                break
    field_ra, field_dec = factor.directions.xy2radec([field_x], [field_y],
                                                     refRA=midRA,
                                                     refDec=midDec)
    field = Direction('field',
                      field_ra[0],
                      field_dec[0],
                      factor_working_dir=directions_list[0].working_dir)
    directions_list.append(field)

    ax.set_title('Overview of Factor run in\n{}'.format(
        directions_list[0].working_dir))

    # Plot facets
    markers = []
    for direction in directions_list:
        if direction.name != 'field':
            vertices = read_vertices(direction.vertices_file)
            RAverts = vertices[0]
            Decverts = vertices[1]
            xverts, yverts = factor.directions.radec2xy(RAverts,
                                                        Decverts,
                                                        refRA=midRA,
                                                        refDec=midDec)
            xyverts = [np.array([xp, yp]) for xp, yp in zip(xverts, yverts)]
            mpl_poly = Polygon(np.array(xyverts),
                               edgecolor='#a9a9a9',
                               facecolor='#F2F2F2',
                               clip_box=ax.bbox,
                               picker=3.0,
                               linewidth=2)
        else:
            xverts = [field_x]
            yverts = [field_y]
            mpl_poly = Circle((field_x, field_y),
                              radius=5.0,
                              edgecolor='#a9a9a9',
                              facecolor='#F2F2F2',
                              clip_box=ax.bbox,
                              picker=3.0,
                              linewidth=2)
        mpl_poly.facet_name = direction.name
        mpl_poly.completed_ops = get_completed_ops(direction)
        mpl_poly.started_ops = get_started_ops(direction)
        mpl_poly.current_op = get_current_op(direction)
        set_patch_color(mpl_poly, direction)
        ax.add_patch(mpl_poly)

        # Add facet names
        if direction.name != 'field':
            poly_tuple = tuple([(xp, yp) for xp, yp in zip(xverts, yverts)])
            xmid = SPolygon(poly_tuple).centroid.x
            ymid = SPolygon(poly_tuple).centroid.y
        else:
            xmid = field_x
            ymid = field_y
        if trim_names:
            name = direction.name.split('_')[-1]
        else:
            name = direction.name
        marker = ax.text(xmid,
                         ymid,
                         name,
                         color='k',
                         clip_on=True,
                         clip_box=ax.bbox,
                         ha='center',
                         va='bottom')
        marker.set_zorder(1001)
        markers.append(marker)

    # Add info box
    at = AnchoredText("Selected direction: None",
                      prop=dict(size=12),
                      frameon=True,
                      loc=3)
    at.patch.set_boxstyle("round,pad=0.,rounding_size=0.2")
    at.set_zorder(1002)
    ax.add_artist(at)

    ax.relim()
    ax.autoscale()
    ax.set_aspect('equal')

    if hasWCSaxes:
        RAAxis = ax.coords['ra']
        RAAxis.set_axislabel('RA', minpad=0.75)
        RAAxis.set_major_formatter('hh:mm:ss')
        DecAxis = ax.coords['dec']
        DecAxis.set_axislabel('Dec', minpad=0.75)
        DecAxis.set_major_formatter('dd:mm:ss')
        ax.coords.grid(color='black', alpha=0.5, linestyle='solid')
    else:
        plt.xlabel("RA (arb. units)")
        plt.ylabel("Dec (arb. units)")

    # Define coodinate formater to show RA and Dec under mouse pointer
    ax.format_coord = formatCoord

    # Show legend
    not_processed_patch = plt.Rectangle((0, 0),
                                        1,
                                        1,
                                        edgecolor='#a9a9a9',
                                        facecolor='#F2F2F2',
                                        linewidth=2)
    processing_patch = plt.Rectangle((0, 0),
                                     1,
                                     1,
                                     edgecolor='#a9a9a9',
                                     facecolor='#F2F5A9',
                                     linewidth=2)
    selfcal_ok_patch = plt.Rectangle((0, 0),
                                     1,
                                     1,
                                     edgecolor='#a9a9a9',
                                     facecolor='#A9F5A9',
                                     linewidth=2)
    selfcal_not_ok_patch = plt.Rectangle((0, 0),
                                         1,
                                         1,
                                         edgecolor='#a9a9a9',
                                         facecolor='#A4A4A4',
                                         linewidth=2)
    processing_error = plt.Rectangle((0, 0),
                                     1,
                                     1,
                                     edgecolor='#a9a9a9',
                                     facecolor='#F5A9A9',
                                     linewidth=2)
    patch_list = [
        not_processed_patch, processing_patch, processing_error,
        selfcal_not_ok_patch, selfcal_ok_patch
    ]
    label_list = [
        'Unprocessed', 'Processing', 'Pipeline Error', 'Selfcal Failed',
        'Selfcal OK'
    ]
    for i in range(options['reimages']):
        label_list.append('Image ' + str(i + 1))
        color = (0.66 / (i + 2)**0.5, 0.96 / (i + 2)**0.5, 0.66 / (i + 2)**0.5,
                 1.0)
        reimage_patch = plt.Rectangle((0, 0),
                                      1,
                                      1,
                                      edgecolor='#a9a9a9',
                                      facecolor=color,
                                      linewidth=2)
        patch_list.append(reimage_patch)
    l = ax.legend(patch_list, label_list, loc="upper right")
    l.set_zorder(1002)

    # Add check for mouse clicks and key presses
    fig.canvas.mpl_connect('pick_event', on_pick)
    fig.canvas.mpl_connect('key_press_event', on_press)

    # Add timer to update the plot every 60 seconds
    timer = fig.canvas.new_timer(interval=60000)
    timer.add_callback(update_plot)
    timer.start()

    # Show plot
    plt.show()
    plt.close(fig)

    # Clean up any temp casacore images
    if not hasaplpy:
        if os.path.exists('/tmp/tempimage'):
            try:
                shutil.rmtree('/tmp/tempimage')
            except OSError:
                pass
Example #4
0
def plot(LSM, fileName=None, labelBy=None):
    """
    Shows a simple plot of the sky model.

    The circles in the plot are scaled with flux. If the sky model is grouped
    into patches, sources are colored by patch and the patch positions are
    indicated with stars.

    Parameters
    ----------
    LSM : SkyModel object
        Input sky model
    fileName : str, optional
        If given, the plot is saved to a file instead of displayed
    labelBy : str, optional
        One of 'source' or 'patch': label points using source names ('source') or
        patch names ('patch')

    Examples:
    ---------
    Plot and display to the screen::

        >>> LSM = lsmtool.load('sky.model')
        >>> plot(LSM)

    Plot and save to a PDF file::

        >>> plot(LSM, 'sky_plot.pdf')

    """
    try:
        import os
        if 'DISPLAY' not in os.environ:
            import matplotlib
            if matplotlib.get_backend() is not 'Agg':
                matplotlib.use("Agg")
        import matplotlib.pyplot as plt
        from matplotlib.ticker import FuncFormatter
    except Exception as e:
        raise ImportError('PyPlot could not be imported. Plotting is not '
            'available: {0}'.format(e.message))
    try:
        try:
            from astropy.visualization.wcsaxes import WCSAxes
            hasWCSaxes = True
        except:
            from wcsaxes import WCSAxes
            hasWCSaxes = True
    except:
        hasWCSaxes = False
    import numpy as np
    from ..operations_lib import radec2xy, makeWCS
    global midRA, midDec, ymin, xmin

    if len(LSM) == 0:
        log.error('Sky model is empty.')
        return

    fig = plt.figure(1,figsize=(7.66,7))
    plt.clf()
    x, y, midRA, midDec  = LSM._getXY()
    if hasWCSaxes:
        wcs = makeWCS(midRA, midDec)
        ax = WCSAxes(fig, [0.16, 0.1, 0.8, 0.8], wcs=wcs)
        fig.add_axes(ax)
    else:
        ax = plt.gca()
    if LSM.hasPatches:
        nsrc = len(LSM.getPatchNames())
    else:
        nsrc = len(LSM)
    sm = plt.cm.ScalarMappable(cmap=plt.cm.Set3, norm=plt.Normalize(vmin=0,
        vmax=nsrc))
    sm._A = []

    # Set symbol sizes by flux, making sure no symbol is smaller than 50 or
    # larger than 1000
    s = []
    fluxes = LSM.getColValues('I')
    if len(fluxes[fluxes > 0.0]) == 0:
        minflux = 0.0
    else:
        minflux = np.min(fluxes[fluxes > 0.0])
    for flux in LSM.getColValues('I'):
        if flux > 0.0:
            s.append(min(1000.0, (1.0+2.0*np.log10(flux/minflux))*50.0))
        else:
            s.append(50.0)

    # Color sources by patch if grouped
    c = [0]*len(LSM)
    cp = []
    if LSM.hasPatches:
        for p, patchName in enumerate(LSM.getPatchNames()):
            indices = LSM.getRowIndex(patchName)
            cp.append(sm.to_rgba(p))
            for ind in indices:
                c[ind] = sm.to_rgba(p)
    else:
        c = [sm.to_rgba(0)] * nsrc

    # Plot sources
    if hasWCSaxes:
        RA = LSM.getColValues('Ra')
        Dec = LSM.getColValues('Dec')
        ax.set_xlim(np.min(x)-20, np.max(x)+20)
        ax.set_ylim(np.min(y)-20, np.max(y)+20)
    plt.scatter(x, y, s=s, c=c)

    if LSM.hasPatches:
        RAp, Decp = LSM.getPatchPositions(asArray=True)
        goodInd = np.where( (RAp != 0.0) & (Decp != 0.0) )
        if len(goodInd[0]) < len(RAp):
            log.info('Some patch positions are unset. Run setPatchPositions() '
                'before plotting to see patch positions and patch names.')
        xp, yp = radec2xy(RAp[goodInd], Decp[goodInd], midRA, midDec)
        plt.scatter(xp, yp, s=100, c=cp, marker='*')

    # Set axis labels, etc.
    if hasWCSaxes:
        RAAxis = ax.coords['ra']
        RAAxis.set_axislabel('RA', minpad=0.75)
        RAAxis.set_major_formatter('hh:mm:ss')
        DecAxis = ax.coords['dec']
        DecAxis.set_axislabel('Dec', minpad=0.75)
        DecAxis.set_major_formatter('dd:mm:ss')
        ax.coords.grid(color='black', alpha=0.5, linestyle='solid')
    else:
        plt.xlabel("RA (arb. units)")
        plt.ylabel("Dec (arb. units)")

    if labelBy is not None:
        if labelBy.lower() == 'source':
            labels = LSM.getColValues('name')
            xls = x
            yls = y
        elif labelBy.lower() == 'patch':
            if LSM.hasPatches:
                labels = LSM.getPatchNames()
                xls = xp
                yls = yp
            else:
                labels = LSM.getColValues('name')
                xls = x
                yls = y
        else:
            raise ValueError("The lableBy parameter must be one of 'source' or "
                "'patch'.")
        for label, xl, yl in zip(labels, xls, yls):
            plt.annotate(label, xy = (xl, yl), xytext = (-2, 2), textcoords=
                'offset points', ha='right', va='bottom')

    # Define coodinate formater to show RA and Dec under mouse pointer
    RAformatter = FuncFormatter(RAtickformatter)
    ax.format_coord = formatCoord

    if fileName is not None:
        plt.savefig(fileName)
    else:
        plt.show()
    plt.close(fig)