import matplotlib as mpl
mpl.use('Agg')
import yt
import trident
import numpy as np
from spectacle.fitting import LineFinder1D
from sys import argv, path
import matplotlib.pyplot as plt
from matplotlib.ticker import AutoMinorLocator
from mpl_toolkits.axes_grid1 import AxesGrid
from numpy.linalg import norm
import astropy.units  as u

from yt.data_objects.static_output import \
    Dataset

from salsa.utils.functions import ion_p_num
from salsa.utils.defaults import default_units_dict, default_limits_dict, default_cloud_dict
from salsa.absorber_extractor import AbsorberExtractor

class AbsorberPlotter(AbsorberExtractor):
    """
    Create's plot to easily see where absorbers are found along the light ray
    both directly and through resulting spectra. Uses absorber extractor as base
    class.

    Parameters
    ----------

    ds_filename: str or YT dataset
        Either Path/name of the dataset to be loaded or the dataset itself

    ray_filename: str or Trident ray
        Path/name of the hdf5 ray file to be loaded or the ray already loaded

    ion_name: string, optional
        Name of the ion to extract absorbers of and plot
        Default: "H I"

    cut_region_filters : list of str, optional
        a list of filters defined by the way you use Cut Regions in YT

    slice_field : string, optional
        Field to plot in slice plot. defaults to ion_name's number density

    absorber_fields : list of strings, optional
        Additional ions to include in plots/Spectra, enter as list.

    north_vector : array type, optional
        vector used to fix the orientation of the slice plot defaults to z-axis

    center_gal : array type, optional
        center of galaxy in code_length. if None, then defaults to domain_center

    wavelength_center : float, optional
        Wavelength to center spectrum plot on. defaults to the stringest known
        spectral line of ion_name. in units of Angstrom

    wavelength_width :float, optional
        sets the wavelength range of the spectrum plot. defaults to 300 Angstroms

    velocity_width :float, optional
        sets the velocity range in spectrum plot in units of km/s

    wavelegnth_res :float, optional
        width of wavelength bins in spectrum plot. default 0.1 Angstrom

    velocity_res :float, optional
        width of velocity bins in spectrum plot. default 10 km/s

    use_spectacle : bool, optional
        Choose whether to use spectacle fit to compute col dense

    plot_spectacle: bool, optional
        chooses whether individual absorption lines found by spectacle are plotted

    spectacle_res : double, optional
        Set minimum resolution that spectacle will attempt to fit lines to. If
        None, default to velocity_res

    plot_spice : bool, optional
        Sets whether the intervals found by the SPICE method are plotted on the
        number density plot

    absorber_min: float, optional
        Minimum Log Column Density that will be used to define an absorber.
        If None, defaults to either default for specific ion or 13
        Default: None

    frac: float, optional
        Parameter defining what fraction of the number density is being
        accounted for in each iteration of the SPICE method. Must be a number
        between 0 and 1.
        Default: 0.8

    num_dense_min: float, optional
        Sets the lower limit for the number density plot. If None, defaults to
        0.01 times the median number density

    num_dense_max: float, optional
        Sets the upper limit for the number density plot. If None, defaults to
        100 times the median number density

    markers :bool, optional
        whether to include markers on light ray and number density plot

    mark_plot_args : dict, optional
        set the property of markers if they are to be plotted.
        optional settings are:

        `marker_spacing`: determines how far apart markers are in kpc.

        `marker_shape`: shape of marker see matplotlib for notation

        `marker_cmap`: colormap used to differentiate markers any other property that can be passer to matplotlib scatter

    figure :matplotlib figure, optional
        where the multi_plot will be plotted. creates one if none is specified.


    Notes
    ------
    ion names should be in following notaion: neutral Hydrogen-->"H I",
    5-times ionized Oxygen --> "O VI"
    """

    def __init__(self,
                ds_filename,
                ray_filename,
                ion_name='H I',
                ftype='gas',
                cut_region_filters=None,
                slice_field=None,
                absorber_fields=[],
                north_vector=[0, 0, 1],
                center_gal = None,
                wavelength_center=None,
                wavelength_width = 30,
                velocity_width = 3000,
                wavelength_res = 0.1,
                velocity_res = 10,
                use_spectacle=False,
                plot_spectacle=False,
                spectacle_defaults=None,
                spectacle_res=None,
                plot_spice=False,
                absorber_min=None,
                frac=0.8,
                num_dense_min=None,
                num_dense_max=None,
                markers=True,
                mark_plot_args=None,
                figure=None):
        #set file names and ion name
        if isinstance(ds_filename, str):
            self.ds = yt.load(ds_filename)
        elif isinstance(ds_filename, Dataset):
            self.ds = ds_filename
        self.ray_filename = ray_filename
        self.ion_name = ion_name

        self.cut_region_filters = cut_region_filters
        self.frac = frac

        #add ion name to list of all ions to be plotted
        self.ion_list = [ion_name] + absorber_fields

        #add ion fields to dataset if not already there
        trident.add_ion_fields(self.ds, ions=self.ion_list, ftype=ftype)

        #set a value for slice
        self.slice = None
        self.north_vector = north_vector
        self.center_gal= center_gal

        #open up the ray files
        self.load_ray(self.ray_filename)


        #set slice field to ion name if no field is specified
        if (slice_field is None):
            self.slice_field = ion_p_num(self.ion_name)
        else:
            self.slice_field = slice_field

        # whether to use/plot these methods
        self.plot_spice = plot_spice
        self.use_spectacle = use_spectacle
        self.plot_spectacle = plot_spectacle

        if absorber_min is None:

            if self.ion_name in default_cloud_dict.keys():
                self.absorber_min = default_cloud_dict[self.ion_name]
            else:
                self.absorber_min=13
        else:
            self.absorber_min = absorber_min

        # define defaults for spectacle fit
        self.defaults_dict = {
            'bounds' :{
                'column_density' : (self.absorber_min-0.5, 23)
            },
            'fixed' : {
                'delta_lambda' : True,
                'column_density' : False
            }
        }

        #add user defined defaults
        if spectacle_defaults is not None:
            self.defaults_dict.update(spectacle_defaults)

        #parameters for trident
        self.wavelength_width = wavelength_width
        self.wavelegnth_res = wavelength_res
        self.velocity_width = velocity_width
        self.velocity_res = velocity_res

        #default spectacle resolution to velocity_res
        if spectacle_res is None:
            self.spectacle_res = velocity_res
        else:
            self.spectacle_res = spectacle_res

        #default set the wavelength center to one of the known spectral lines
        #for ion name. Use tridents line database to search for correct wavelength
        if wavelength_center is None:
            #open up tridents default line database
            lbd = trident.LineDatabase('lines.txt')
            #find all lines that match ion
            lines = lbd.parse_subset(subsets= [self.ion_name])
            #take one with largest f_value
            f_val = 0
            for line in lines:
                if line.f_value >= f_val:
                    f_val = line.f_value
                    self.wavelength_center = line.wavelength
        else:
            self.wavelength_center = wavelength_center

        #open up a figure if none specified
        if figure is None:
            self.fig = plt.figure(figsize=(10, 10))
        else:
            self.fig = figure


        #set marker plot properties
        self.markers = markers
        if markers:
            self.mark_kwargs = {'alpha' : 0.45,
                                's' : 100,
                                'edgecolors' : 'black',
                                'linewidth' : 3,
                                'spacing' :50,
                                'marker_cmap' : 'viridis',
                                'marker_shape' :'s'}
            if mark_plot_args != None:
                self.mark_kwargs.update(mark_plot_args)

            self.marker_spacing = self.mark_kwargs.pop('spacing')
            self.marker_cmap = self.mark_kwargs.pop('marker_cmap')
            self.marker_shape = self.mark_kwargs.pop('marker_shape')
        self.mark_dist_arr = None

        #optionally set min/max value for number density plot
        self.num_dense_min = num_dense_min
        self.num_dense_max = num_dense_max



    def add_annotations(self, plot=True):
        """
        Adds ray and marker annotations to slice plot

        Parameters
        -----------
        plot : bool
            Whether to annotate ray/markers to the slice plot or to just
            calculate the marker positions for placing on los_velocity plot
        """

        if plot:
            #annotate ray
            self.slice.annotate_ray(self.ray, arrow=True, plot_args={'alpha':0.5, 'color':'white', 'linewidth':2})

        if self.markers:
            #get ray positional properties
            ray_begin, ray_end, ray_length, ray_direction = self.ray_position_prop(units='kpc')
            #make marker every x kpc. skip start
            mark_dist = self.marker_spacing #kpc
            mark_dist_arr = np.arange(mark_dist, ray_length.value, mark_dist)
            self.mark_dist_arr = self.ds.arr(mark_dist_arr, 'kpc')

            #define colormap and scale
            mrk_cmap = plt.cm.get_cmap(self.marker_cmap)
            self.colorscale = np.linspace(0, 1, mark_dist_arr.size)

            if plot:
                #construct unit vec from ray
                for i in range(mark_dist_arr.size):
                    #calculate the position
                    mrk_pos = ray_begin + ray_direction * self.mark_dist_arr[i]

                    #choose correct color from cmap
                    mrk_kwargs = self.mark_kwargs.copy()
                    mrk_kwargs['color'] = mrk_cmap(self.colorscale[i])

                    self.slice.annotate_marker(mrk_pos, marker=self.marker_shape, plot_args=mrk_kwargs)

    def create_slice(self, cmap="magma", height=None, width=None):
        """
        Create a slice in the Dataset along the path of the ray.
        Choose to keep the Z direction maintained.

        Parameters
        ----------

        cmap: str
            the colormap to use for the slice. Default: 'magma'

        Returns
        -------
        slice : yt SlicePlot
            Slice with ray annotated
        """
        #print("adding ion fields")

        # runs way to slow, may add later
        if False: #self.cut_region_filters is not None:
            # parse for radial cuts
            rad_in, rad_out, cut_str = self.cgm_details
            cgm = self.ds.sphere(self.center_gal, (rad_out, 'kpc')) \
                  - self.ds.sphere(self.center_gal, (rad_in, 'kpc'))
            # cuts running too slow rn so just not including them
            data_source = cgm.cut_region(cut_str)
        else:
            data_source=None

        ray_begin, ray_end, ray_length, ray_unit = self.ray_position_prop(units='kpc')

        #construct vec orthogonal to ray/plane
        self.north_vector = self.ds.arr(self.north_vector, 'dimensionless')
        norm_vector = np.cross(ray_unit, self.north_vector)
        norm_vector = norm_vector/np.linalg.norm(norm_vector)

        #set center to domain_center unless specified
        if self.center_gal is None:
            self.center_gal = self.ds.domain_center
        else:
            self.center_gal = self.ds.arr(self.center_gal, 'code_length')

        #adjust center so that it is in the plane of ray and north_vector
        ray_center = (ray_begin + ray_end)/2
        ray_center = ray_center.in_units('code_length')
        center_dif = ray_center - self.center_gal
        scale = self.ds.quan(np.dot(center_dif, norm_vector), 'code_length')
        center = scale*norm_vector + self.center_gal

        #set width/height
        if width ==None and height==None:
            #default to length of ray
            wid_hght=ray_length
        elif width ==None and height != None:
            #width still defaults to length of ray
            wid_hght=((ray_length.to_value(), 'kpc'), (height, 'kpc'))
        elif width != None and height ==None:
            wid_hght= ((width, 'kpc'), (ray_length.to_value(), 'kpc'))
        else:
            wid_hght= ((width, 'kpc'), (height, 'kpc'))

        #Create slice along ray. keep slice pointed in north_Vec direction
        self.slice = yt.OffAxisSlicePlot(self.ds,
                          norm_vector,
                          self.slice_field,
                          center=center,
                          north_vector = self.north_vector,
                          width = wid_hght,
                          data_source=data_source)



        #set axes to kpc
        self.slice.set_axes_unit('kpc')

        #annotate plot
        self.add_annotations()

        # set color map
        self.slice.set_cmap(field=self.slice_field, cmap = cmap)

        # set background to bottom of color map
        self.slice.set_background_color(self.slice_field)

        return self.slice

    def plot_vel_space(self, ax=None, annotate_column_density=True):
        """
        Use trident to plot the absorption spectrum of the ray in velocity
        space. Compute column densities with spectacle fits.

        Parameters
        -----------
        ax: matplotlib axis object, optional
            an axis in which to draw the velocity plot. If None, no plot is
            not drawn.
            Default: None

        annotate_column_density: bool, optional
            if True, add a textbox reporting the calculated col densities
            by each method to the plot.
            Default: True

        Returns
        ----------
            velocity: YT array
                Array of velocity values of the generated spectra (in km/s)

            flux: YT array
                Array of the normalized flux values of the generated spectra

        """

        # add wav center first so it is set as zero point velocity by trident
        wav = int( np.round(self.wavelength_center) )
        line = f"{self.ion_name} {wav}"
        ion_list = [line] + self.ion_list

        #set up spectra
        vel_min = -self.velocity_width/2
        vel_max = self.velocity_width/2
        spect_gen = trident.SpectrumGenerator(lambda_min=vel_min,
                                              lambda_max=vel_max,
                                              dlambda = self.velocity_res,
                                              bin_space="velocity")

        #generate spectra and return fields
        spect_gen.make_spectrum(self.data, lines=ion_list)
        flux = spect_gen.flux_field
        velocity = spect_gen.lambda_field.in_units('km/s')

        if ax is not None:
            #plot values for velocity plot
            ax.plot(velocity[:-1], flux[:-1])
            ax.set_ylim(0, 1.05)
            ax.set_xlim(vel_min, vel_max)
            ax.xaxis.set_minor_locator(AutoMinorLocator(2))
            ax.set_title(f"Rel. to line {self.wavelength_center:.1f} $\AA$", loc='right')
            ax.set_xlabel("Delta_v (km/s)")
            ax.set_ylabel("Flux")
            ax.grid(zorder=0, which='both')

            if self.use_spectacle:
                line_txt, line_models = self._get_vel_plot_annotations()
                box_props = dict(boxstyle='square', facecolor='white')

                if annotate_column_density:
                    #annotate plot with column densities
                    ax.text(0.8, 0.05, line_txt, transform=ax.transAxes, bbox = box_props)

                #annotate number of lines
                ax.text(0.9, 0.85, f"{self.num_spectacle} lines", transform=ax.transAxes, bbox = box_props)

                colors = ['tab:purple', 'tab:orange', 'tab:green']
                vel= np.linspace(vel_min, vel_max, 1000) *u.Unit('km/s')
                #plot individual column lines
                if line_models is not None:
                    for mod, color in zip(line_models, colors):
                        #plot centroids of largest lines
                        dv = mod.lines[0].delta_v.value
                        cd = mod.lines[0].column_density.value
                        ax.scatter(dv, 1, c=color, marker='v',zorder=5, label="logN={:04.1f}".format(cd))
                        #plott the largest lines
                        if self.plot_spectacle:
                            ax.step(vel, mod(vel), linestyle='--', color=color, alpha=0.75)
                    ax.legend(loc='lower left')


        return velocity, flux

    def plot_lambda_space(self, ax=None):
        """
        Use trident to plot the absorption spectrum of the ray. Plot in
        wavelegnth (lambda) space. Not formatted to be used in spectacle fitting

        Parameters
        -----------
        ax : matplotlib axis
            axis in which to draw the spectra plot

        Returns
        --------
            wavelength: YT array
                Array of wavelength values of the generated spectra (in km/s)

            flux: YT array
                Array of the normalized flux values of the generated spectra
        """
        #set which ions to add to spectra
        ion_list = self.ion_list

        #adjust wavelegnth_center for redshift
        rest_wavelength = self.wavelength_center
        wave_min = rest_wavelength - self.wavelength_width/2
        wave_max = rest_wavelength + self.wavelength_width/2

        #use wavelength_width to set the range
        spect_gen = trident.SpectrumGenerator(lambda_min=wave_min, lambda_max=wave_max, dlambda = self.wavelegnth_res)
        spect_gen.make_spectrum(self.data, lines=ion_list, observing_redshift=self.ds.current_redshift)


        #get fields from spectra and give correct units
        rest_wavelength = rest_wavelength*u.Unit('angstrom')
        wavelength = spect_gen.lambda_field * u.Unit('angstrom')
        flux = spect_gen.flux_field

        if ax is not None:
            #plot values for spectra
            ax.plot(wavelength[:-1], flux[:-1])
            ax.set_ylim(0, 1.05)
            ax.set_xlim(wave_min, wave_max)
            ax.xaxis.set_minor_locator(AutoMinorLocator(2))
            ax.set_title(f"Spectrum {self.ion_name}", loc='right')
            ax.set_xlabel("Wavelength $\AA$")
            ax.set_ylabel("Flux")
            ax.grid(zorder=0, which='both')

        return wavelength, flux

    def plot_num_density(self, ax_num_dense, ax_prop2=None,
                         prop2_name='velocity_los', prop2_units=None,
                         plot_kwargs={}):
        """
        Plots the number density at different lengths along the ray

        Parameters
        ----------
        ax_num_dense : matplotlib axis
            axis in which to draw the number density plot

        ax_prop2: matplotlib axis, optional
            axis in which to draw the second field. if None, no plot is made
            Default: None

        prop2_name: str,optional
            Field to plot in second plot.
            Default:'velocity_los'

        prop2_units: str, optional
            The units to use in the second field.
            Defaults: None
        plot_kwargs: dict, optional
            A Dictionary of plot kwargs to be passed to the pyplot.plot function.
            Default: {}
        """
        #get list of num density  los velocity and corresponding lengths
        num_density = self.data[ion_p_num(self.ion_name)]
        prop2 = self.data[prop2_name]

        prop2_lb = None
        prop2_ub = None

        #load defaults for prop2
        if prop2_units is None:

            #check if defaults for field
            if prop2_name in default_units_dict.keys():
                prop2_units = default_units_dict[prop2_name]
                prop2 = prop2.in_units(prop2_units)

                # set default bounds
                if prop2_name in default_limits_dict.keys():
                    prop2_lb, prop2_ub = default_limits_dict[prop2_name]

            else:
                # use default of trident (genarlly in cgs units)
                prop2_units = str(prop2.units)
        else:
            # convert to specified units
            prop2 = prop2.in_units(prop2_units)

        #get length data and define x limits
        l_list = self.data['l'].in_units('kpc')
        full_l = self.uncut_data['l'].in_units('kpc')
        pad = 0.1*full_l[-1]
        xlimits = [-pad, full_l[-1] + pad]

        # check if l_list is non-empty cuz something went wrong then.
        if l_list.size == 0:
            err_file = open("error_file.txt", 'a')
            err_file.write(f"{self.ray_filename} had an l_list that was of size zero")
            err_file.close()
            return 1

        if ax_num_dense is not None:
            #make num density plots
            ax_num_dense.plot(l_list, num_density, **plot_kwargs)
            ax_num_dense.set_title(f"Number Density of {self.ion_name} Along Ray", loc='right')
            ax_num_dense.set_xlabel("Length From Start of Ray $(kpc)$")
            ax_num_dense.set_ylabel("Number Density \n$(cm^{-3})$")
            ax_num_dense.set_yscale('log')
            ax_num_dense.grid(zorder=0)

            #chech if min/max num dense was called
            if (self.num_dense_min is None and self.num_dense_max is None):
                med = np.median(num_density)
                self.num_dense_min = med*0.01
                self.num_dense_max = med*1000

            #set axes limits
            ax_num_dense.set_ylim(self.num_dense_min, self.num_dense_max)
            ax_num_dense.set_xlim(xlimits[0], xlimits[1])
            #add minor tick marks
            ax_num_dense.xaxis.set_minor_locator(AutoMinorLocator(2))

            #check if should plot spice intervals
            if self.plot_spice:
                # run spice method if not already run
                if self.num_spice is None:
                    self.get_spice_absorbers()

                #plot spice intervals
                if self.num_spice > 0:
                    for i in range(self.num_spice):
                        b, e = self.spice_intervals[i]
                        curr_lcd = self.spice_df.loc[i, 'col_dens']

                        #plot interval
                        ax_num_dense.axvspan(l_list[b], l_list[e], alpha=0.5, edgecolor='black',facecolor='tab:grey')#vspan_cmap((curr_lcd-12)/11))

                        #plot on 2nd prop if axis exists
                        if ax_prop2 is not None:
                            ax_prop2.axvspan(l_list[b], l_list[e], alpha=0.5, edgecolor='black',facecolor='tab:grey')#vspan_cmap((curr_lcd-12)/11))

                    #plot number of intervals found
                    box_props = dict(boxstyle='square', facecolor='white')
                    ax_num_dense.text(0.9, 0.85, f"{self.num_spice} feat.", transform=ax_num_dense.transAxes, bbox = box_props)

                    #take three largest absorbers and sort by position
                    max_indices = self.spice_df['col_dens'].argsort()
                    max_indices = max_indices[-3:].to_numpy()
                    max_indices.sort()

                    #plot markers from left to right
                    colors=['black', 'magenta', 'yellow']
                    for i,c in zip(max_indices, colors):
                        b, e = self.spice_intervals[i]
                        lcd = self.spice_df.loc[i, 'col_dens']
                        mid_point = (l_list[b]+l_list[e])/2

                        ax_num_dense.scatter(mid_point, 0.75*self.num_dense_max,
                                             marker='v',color=c, edgecolors='black',
                                             label=f"logN={lcd:.1f}", zorder=3)

                    ax_num_dense.legend(loc='lower left', bbox_to_anchor=(-0.015, 0.95))

        #make second plot
        if ax_prop2 is not None:
            #plot zero mark if line of sight velocity
            if ax_prop2 == 'los_velocity':
                ax_prop2.hlines(0, l_list[0], l_list[-1], linestyles='dashed',alpha=0.25, zorder=1)

            ax_prop2.plot(l_list, prop2, **plot_kwargs)

            #set title and axis labels
            ax_prop2.set_title(f"{prop2_name} Along Ray", loc='right')
            ax_prop2.set_xlabel("Length From Start of Ray $(kpc)$")
            ax_prop2.set_ylabel(f"{prop2_name} $({prop2_units})$")

            #set limits
            ax_prop2.set_ylim(prop2_lb, prop2_ub)
            ax_prop2.set_xlim(xlimits[0], xlimits[1])

            #set minor ticks and grid lines
            ax_prop2.yaxis.set_minor_locator(AutoMinorLocator(2))
            ax_prop2.xaxis.set_minor_locator(AutoMinorLocator(2))
            ax_prop2.grid(zorder=0, which='major')
            ax_prop2.grid(zorder=0, which='minor', axis='y')

        #add appropriate markers to the plot
        if self.markers and ax_prop2 is not None:
            #check if marker distances have been defined
            if self.mark_dist_arr is None:
                self.add_annotations(plot=False)

            Vys = np.zeros_like(self.mark_dist_arr) - 500
            plot_markers = {}
            plot_markers.update(self.mark_kwargs)
            ax_prop2.scatter(self.mark_dist_arr.value, Vys,zorder=3, c=self.colorscale, marker=self.marker_shape, cmap=self.marker_cmap, **plot_markers)

    def create_multi_plot(self, outfname=None, markers=True, cmap="magma"):
        """
        combines the slice plot, number density plot, and spectrum plot into
        one image.

        Parameters
        -----------
        outfname: str , optional
            the file name/path in which to save the file defaults to being unsaved.
            Default: None

        markers: bool, optional
            adds markers to slice plot and number density to aid analysis between those plots.
            Default: True

        cmap:  Colormap, optional
            the color map to use for the slice plot.
            Default: magma

        Returns
        ---------
        fig : matplotlib figure:
            figure multi_plot is drawn on
        axes : matplotlib axes
            axes the three lower plots are drawn on
        """

        if (self.slice == None):
            #create the slicePlot using the field of the ion density
            self.create_slice(cmap = cmap)

        grid = AxesGrid(self.fig, (0.,0.,0.5,0.5),
                        nrows_ncols = (1, 1),
                        axes_pad = 0.5,
                        label_mode = "L",
                        share_all = False,
                        cbar_location="right",
                        cbar_mode="each",
                        cbar_size="3%",
                        cbar_pad="0%")

        #redraw slice plot onto figure
        plot = self.slice.plots[self.slice_field]
        plot.figure = self.fig
        plot.axes = grid[0].axes
        plot.cax = grid.cbar_axes[0]

        self.slice._setup_plots()

        #set up axes and draw other plots to them
        ax1 = self.fig.add_subplot(411)
        ax2 = self.fig.add_subplot(412)
        ax3 = self.fig.add_subplot(413)

        self.plot_num_density(ax1, ax_prop2=ax2)
        self.plot_vel_space(ax=ax3)

        axes= [ax1, ax2, ax3]
        #setup positioning for the plots underneath
        strt_pos = -0.255
        ax1.set_position( [0.0, strt_pos, 0.5, 0.15] )
        ax2.set_position( [0.0, strt_pos-0.16, 0.5, 0.15] )
        ax3.set_position( [0.0, strt_pos-0.4, 0.5, 0.15] )

        #set num dense and los vel to share axis
        ax1.set_xlabel("")
        ax2.set_title("", loc='right')
        ax1.get_shared_x_axes().join(ax1, ax2)
        ax1.set_xticklabels([])
        if (outfname != None):
            self.fig.savefig(outfname, bbox_inches='tight')

        return self.fig, axes

    def zoom(self, factor):
        """
        Zoom into the slice by specified factor

        Parameters
        ----------
        factor : float
            factor by which to zoom in using yt's zoom mehtod

        """

        self.slice.zoom(factor)

    def close(self):
        """
        close all opened files
        """

        self.ds.close()
        self.ray.close()
        plt.close(self.fig)

    def _get_vel_plot_annotations(self):
        """
        computes the column density along the given ray for a given ion species.
        This is done by using spectacle if use_spectacle is True. as well as
        by summing the product of the number density for a given length by that length.
        and the SPICE method

        Returns:
            line_models : list spectacle models : Individual line models for the
                        3 largest absorbers found by spectacle
            line_text : string : a string of properly formatted col dense to
                        be added on to multi_plot
        """

        # run thw two methods if not already done
        if self.num_spectacle is None:
            # run spectacle method
            self.get_spectacle_absorbers()
        if self.num_spice is None:
            self.get_spice_absorbers()


        fit_label="Spect:"
        #check if no absorbers found
        if self.num_spectacle == 0:
            line_models = None
            fit_string = "{: <14s}{: >4s}\n".format(fit_label, '--')
        else:
            #get total column density and 3 largest lines
            tot_spect_cd, line_models = self._get_large_spectacle()
            fit_string = "{: <14s}{:04.1f}\n".format(fit_label, tot_spect_cd)

        #get sum from SPICE method
        spice_label="SPICE:"
        #check if no absorbers
        if self.num_spice == 0:
            spice_string = "{: <11s}{: >4s}\n".format(spice_label,'--')
        else:
            #find total column density for SPICE method
            cd_sum=0
            for lcd in self.spice_df['col_dens']:
                cd_sum += 10**lcd

            log_cd_sum = np.log10(cd_sum)
            spice_string = "{: <11s}{:04.1f}\n".format(spice_label,log_cd_sum)

        #get total column density along ray
        ion_field = ion_p_num(self.ion_name)
        tot_ray_cd= np.sum( self.data[ion_field].in_units('cm**-3')*self.data['dl'].in_units('cm') )
        log_tot_ray = np.log10(tot_ray_cd)
        total_string="{: <14s}{:04.1f}".format("full ray:", log_tot_ray)

        #combine strings to create "legend"
        line_text = "Tot Sums\n"+spice_string + fit_string + total_string

        return line_text, line_models

    def _get_large_spectacle(self):
        """
        Return the total column density found by spectacle and the 3 largest
        absorbers found by spectacle.
        """
        #compute total column density
        line_sum_cd = 0
        for cd in self.spectacle_df['col_dens']:
            line_sum_cd+= 10**cd
        log_tot_cd = np.log10(line_sum_cd)

        line_models = []
        indx_max = self.spectacle_df['col_dens'].argsort()
        for indx in indx_max[-3:]:
            line = self.spectacle_model.lines[indx]
            line_models.append( self.spectacle_model.with_line(line, reset=True))

        #sort lines based on delta v
        line_models.sort(key=lambda mod: mod.lines[0].delta_v.value)

        return log_tot_cd, line_models

import matplotlib as mpl
mpl.use('Agg')
import yt
import trident
import numpy as np
from spectacle.fitting import LineFinder1D
from sys import argv, path
import matplotlib.pyplot as plt
from matplotlib.ticker import AutoMinorLocator
from mpl_toolkits.axes_grid1 import AxesGrid
from numpy.linalg import norm
import astropy.units  as u

from yt.data_objects.static_output import \
    Dataset

from salsa.utils.functions import ion_p_num
from salsa.utils.defaults import default_units_dict, default_limits_dict, default_cloud_dict
from salsa.absorber_extractor import AbsorberExtractor

class AbsorberPlotter(AbsorberExtractor):
    """
    Create's plot to easily see where absorbers are found along the light ray
    both directly and through resulting spectra. Uses absorber extractor as base
    class.

    Parameters
    ----------

    ds_filename: str or YT dataset
        Either Path/name of the dataset to be loaded or the dataset itself

    ray_filename: str or Trident ray
        Path/name of the hdf5 ray file to be loaded or the ray already loaded

    ion_name: string, optional
        Name of the ion to extract absorbers of and plot
        Default: "H I"

    cut_region_filters : list of str, optional
        a list of filters defined by the way you use Cut Regions in YT

    slice_field : string, optional
        Field to plot in slice plot. defaults to ion_name's number density

    absorber_fields : list of strings, optional
        Additional ions to include in plots/Spectra, enter as list.

    north_vector : array type, optional
        vector used to fix the orientation of the slice plot defaults to z-axis

    center_gal : array type, optional
        center of galaxy in code_length. if None, then defaults to domain_center

    wavelength_center : float, optional
        Wavelength to center spectrum plot on. defaults to the stringest known
        spectral line of ion_name. in units of Angstrom

    wavelength_width :float, optional
        sets the wavelength range of the spectrum plot. defaults to 300 Angstroms

    velocity_width :float, optional
        sets the velocity range in spectrum plot in units of km/s

    wavelegnth_res :float, optional
        width of wavelength bins in spectrum plot. default 0.1 Angstrom

    velocity_res :float, optional
        width of velocity bins in spectrum plot. default 10 km/s

    use_spectacle : bool, optional
        Choose whether to use spectacle fit to compute col dense

    plot_spectacle: bool, optional
        chooses whether individual absorption lines found by spectacle are plotted

    spectacle_res : double, optional
        Set minimum resolution that spectacle will attempt to fit lines to. If
        None, default to velocity_res

    plot_spice : bool, optional
        Sets whether the intervals found by the SPICE method are plotted on the
        number density plot

    absorber_min: float, optional
        Minimum Log Column Density that will be used to define an absorber.
        If None, defaults to either default for specific ion or 13
        Default: None

    frac: float, optional
        Parameter defining what fraction of the number density is being
        accounted for in each iteration of the SPICE method. Must be a number
        between 0 and 1.
        Default: 0.8

    num_dense_min: float, optional
        Sets the lower limit for the number density plot. If None, defaults to
        0.01 times the median number density

    num_dense_max: float, optional
        Sets the upper limit for the number density plot. If None, defaults to
        100 times the median number density

    markers :bool, optional
        whether to include markers on light ray and number density plot

    mark_plot_args : dict, optional
        set the property of markers if they are to be plotted.
        optional settings are:

        `marker_spacing`: determines how far apart markers are in kpc.

        `marker_shape`: shape of marker see matplotlib for notation

        `marker_cmap`: colormap used to differentiate markers any other property that can be passer to matplotlib scatter

    figure :matplotlib figure, optional
        where the multi_plot will be plotted. creates one if none is specified.


    Notes
    ------
    ion names should be in following notaion: neutral Hydrogen-->"H I",
    5-times ionized Oxygen --> "O VI"
    """

    def __init__(self,
                ds_filename,
                ray_filename,
                ion_name='H I',
                ftype='gas',
                cut_region_filters=None,
                slice_field=None,
                absorber_fields=[],
                north_vector=[0, 0, 1],
                center_gal = None,
                wavelength_center=None,
                wavelength_width = 30,
                velocity_width = 3000,
                wavelength_res = 0.1,
                velocity_res = 10,
                use_spectacle=False,
                plot_spectacle=False,
                spectacle_defaults=None,
                spectacle_res=None,
                plot_spice=False,
                absorber_min=None,
                frac=0.8,
                num_dense_min=None,
                num_dense_max=None,
                markers=True,
                mark_plot_args=None,
                figure=None):
        #set file names and ion name
        if isinstance(ds_filename, str):
            self.ds = yt.load(ds_filename)
        elif isinstance(ds_filename, Dataset):
            self.ds = ds_filename
        self.ray_filename = ray_filename
        self.ion_name = ion_name

        self.cut_region_filters = cut_region_filters
        self.frac = frac

        #add ion name to list of all ions to be plotted
        self.ion_list = [ion_name] + absorber_fields

        #add ion fields to dataset if not already there
        trident.add_ion_fields(self.ds, ions=self.ion_list, ftype=ftype)

        #set a value for slice
        self.slice = None
        self.north_vector = north_vector
        self.center_gal= center_gal

        #open up the ray files
        self.load_ray(self.ray_filename)


        #set slice field to ion name if no field is specified
        if (slice_field is None):
            self.slice_field = ion_p_num(self.ion_name)
        else:
            self.slice_field = slice_field

        # whether to use/plot these methods
        self.plot_spice = plot_spice
        self.use_spectacle = use_spectacle
        self.plot_spectacle = plot_spectacle

        if absorber_min is None:

            if self.ion_name in default_cloud_dict.keys():
                self.absorber_min = default_cloud_dict[self.ion_name]
            else:
                self.absorber_min=13
        else:
            self.absorber_min = absorber_min

        # define defaults for spectacle fit
        self.defaults_dict = {
            'bounds' :{
                'column_density' : (self.absorber_min-0.5, 23)
            },
            'fixed' : {
                'delta_lambda' : True,
                'column_density' : False
            }
        }

        #add user defined defaults
        if spectacle_defaults is not None:
            self.defaults_dict.update(spectacle_defaults)

        #parameters for trident
        self.wavelength_width = wavelength_width
        self.wavelegnth_res = wavelength_res
        self.velocity_width = velocity_width
        self.velocity_res = velocity_res

        #default spectacle resolution to velocity_res
        if spectacle_res is None:
            self.spectacle_res = velocity_res
        else:
            self.spectacle_res = spectacle_res

        #default set the wavelength center to one of the known spectral lines
        #for ion name. Use tridents line database to search for correct wavelength
        if wavelength_center is None:
            #open up tridents default line database
            lbd = trident.LineDatabase('lines.txt')
            #find all lines that match ion
            lines = lbd.parse_subset(subsets= [self.ion_name])
            #take one with largest f_value
            f_val = 0
            for line in lines:
                if line.f_value >= f_val:
                    f_val = line.f_value
                    self.wavelength_center = line.wavelength
        else:
            self.wavelength_center = wavelength_center

        #open up a figure if none specified
        if figure is None:
            self.fig = plt.figure(figsize=(10, 10))
        else:
            self.fig = figure


        #set marker plot properties
        self.markers = markers
        if markers:
            self.mark_kwargs = {'alpha' : 0.45,
                                's' : 100,
                                'edgecolors' : 'black',
                                'linewidth' : 3,
                                'spacing' :50,
                                'marker_cmap' : 'viridis',
                                'marker_shape' :'s'}
            if mark_plot_args != None:
                self.mark_kwargs.update(mark_plot_args)

            self.marker_spacing = self.mark_kwargs.pop('spacing')
            self.marker_cmap = self.mark_kwargs.pop('marker_cmap')
            self.marker_shape = self.mark_kwargs.pop('marker_shape')
        self.mark_dist_arr = None

        #optionally set min/max value for number density plot
        self.num_dense_min = num_dense_min
        self.num_dense_max = num_dense_max



    def add_annotations(self, plot=True):
        """
        Adds ray and marker annotations to slice plot

        Parameters
        -----------
        plot : bool
            Whether to annotate ray/markers to the slice plot or to just
            calculate the marker positions for placing on los_velocity plot
        """

        if plot:
            #annotate ray
            self.slice.annotate_ray(self.ray, arrow=True, plot_args={'alpha':0.5, 'color':'white', 'linewidth':2})

        if self.markers:
            #get ray positional properties
            ray_begin, ray_end, ray_length, ray_direction = self.ray_position_prop(units='kpc')
            #make marker every x kpc. skip start
            mark_dist = self.marker_spacing #kpc
            mark_dist_arr = np.arange(mark_dist, ray_length.value, mark_dist)
            self.mark_dist_arr = self.ds.arr(mark_dist_arr, 'kpc')

            #define colormap and scale
            mrk_cmap = plt.cm.get_cmap(self.marker_cmap)
            self.colorscale = np.linspace(0, 1, mark_dist_arr.size)

            if plot:
                #construct unit vec from ray
                for i in range(mark_dist_arr.size):
                    #calculate the position
                    mrk_pos = ray_begin + ray_direction * self.mark_dist_arr[i]

                    #choose correct color from cmap
                    mrk_kwargs = self.mark_kwargs.copy()
                    mrk_kwargs['color'] = mrk_cmap(self.colorscale[i])

                    self.slice.annotate_marker(mrk_pos, marker=self.marker_shape, plot_args=mrk_kwargs)

    def create_slice(self, cmap="magma", height=None, width=None):
        """
        Create a slice in the Dataset along the path of the ray.
        Choose to keep the Z direction maintained.

        Parameters
        ----------

        cmap: str
            the colormap to use for the slice. Default: 'magma'

        Returns
        -------
        slice : yt SlicePlot
            Slice with ray annotated
        """
        #print("adding ion fields")

        # runs way to slow, may add later
        if False: #self.cut_region_filters is not None:
            # parse for radial cuts
            rad_in, rad_out, cut_str = self.cgm_details
            cgm = self.ds.sphere(self.center_gal, (rad_out, 'kpc')) \
                  - self.ds.sphere(self.center_gal, (rad_in, 'kpc'))
            # cuts running too slow rn so just not including them
            data_source = cgm.cut_region(cut_str)
        else:
            data_source=None

        ray_begin, ray_end, ray_length, ray_unit = self.ray_position_prop(units='kpc')

        #construct vec orthogonal to ray/plane
        self.north_vector = self.ds.arr(self.north_vector, 'dimensionless')
        norm_vector = np.cross(ray_unit, self.north_vector)
        norm_vector = norm_vector/np.linalg.norm(norm_vector)

        #set center to domain_center unless specified
        if self.center_gal is None:
            self.center_gal = self.ds.domain_center
        else:
            self.center_gal = self.ds.arr(self.center_gal, 'code_length')

        #adjust center so that it is in the plane of ray and north_vector
        ray_center = (ray_begin + ray_end)/2
        ray_center = ray_center.in_units('code_length')
        center_dif = ray_center - self.center_gal
        scale = self.ds.quan(np.dot(center_dif, norm_vector), 'code_length')
        center = scale*norm_vector + self.center_gal

        #set width/height
        if width ==None and height==None:
            #default to length of ray
            wid_hght=ray_length
        elif width ==None and height != None:
            #width still defaults to length of ray
            wid_hght=((ray_length.to_value(), 'kpc'), (height, 'kpc'))
        elif width != None and height ==None:
            wid_hght= ((width, 'kpc'), (ray_length.to_value(), 'kpc'))
        else:
            wid_hght= ((width, 'kpc'), (height, 'kpc'))

        #Create slice along ray. keep slice pointed in north_Vec direction
        self.slice = yt.OffAxisSlicePlot(self.ds,
                          norm_vector,
                          self.slice_field,
                          center=center,
                          north_vector = self.north_vector,
                          width = wid_hght,
                          data_source=data_source)



        #set axes to kpc
        self.slice.set_axes_unit('kpc')

        #annotate plot
        self.add_annotations()

        # set color map
        self.slice.set_cmap(field=self.slice_field, cmap = cmap)

        # set background to bottom of color map
        self.slice.set_background_color(self.slice_field)

        return self.slice

    def plot_vel_space(self, ax=None, annotate_column_density=True):
        """
        Use trident to plot the absorption spectrum of the ray in velocity
        space. Compute column densities with spectacle fits.

        Parameters
        -----------
        ax: matplotlib axis object, optional
            an axis in which to draw the velocity plot. If None, no plot is
            not drawn.
            Default: None

        annotate_column_density: bool, optional
            if True, add a textbox reporting the calculated col densities
            by each method to the plot.
            Default: True

        Returns
        ----------
            velocity: YT array
                Array of velocity values of the generated spectra (in km/s)

            flux: YT array
                Array of the normalized flux values of the generated spectra

        """

        # add wav center first so it is set as zero point velocity by trident
        wav = int( np.round(self.wavelength_center) )
        line = f"{self.ion_name} {wav}"
        ion_list = [line] + self.ion_list

        #set up spectra
        vel_min = -self.velocity_width/2
        vel_max = self.velocity_width/2
        spect_gen = trident.SpectrumGenerator(lambda_min=vel_min,
                                              lambda_max=vel_max,
                                              dlambda = self.velocity_res,
                                              bin_space="velocity")

        #generate spectra and return fields
        spect_gen.make_spectrum(self.data, lines=ion_list)
        flux = spect_gen.flux_field
        velocity = spect_gen.lambda_field.in_units('km/s')

        if ax is not None:
            #plot values for velocity plot
            ax.plot(velocity[:-1], flux[:-1])
            ax.set_ylim(0, 1.05)
            ax.set_xlim(vel_min, vel_max)
            ax.xaxis.set_minor_locator(AutoMinorLocator(2))
            ax.set_title(f"Rel. to line {self.wavelength_center:.1f} $\AA$", loc='right')
            ax.set_xlabel("Delta_v (km/s)")
            ax.set_ylabel("Flux")
            ax.grid(zorder=0, which='both')

            if self.use_spectacle:
                line_txt, line_models = self._get_vel_plot_annotations()
                box_props = dict(boxstyle='square', facecolor='white')

                if annotate_column_density:
                    #annotate plot with column densities
                    ax.text(0.8, 0.05, line_txt, transform=ax.transAxes, bbox = box_props)

                #annotate number of lines
                ax.text(0.9, 0.85, f"{self.num_spectacle} lines", transform=ax.transAxes, bbox = box_props)

                colors = ['tab:purple', 'tab:orange', 'tab:green']
                vel= np.linspace(vel_min, vel_max, 1000) *u.Unit('km/s')
                #plot individual column lines
                if line_models is not None:
                    for mod, color in zip(line_models, colors):
                        #plot centroids of largest lines
                        dv = mod.lines[0].delta_v.value
                        cd = mod.lines[0].column_density.value
                        ax.scatter(dv, 1, c=color, marker='v',zorder=5, label="logN={:04.1f}".format(cd))
                        #plott the largest lines
                        if self.plot_spectacle:
                            ax.step(vel, mod(vel), linestyle='--', color=color, alpha=0.75)
                    ax.legend(loc='lower left')


        return velocity, flux

    def plot_lambda_space(self, ax=None):
        """
        Use trident to plot the absorption spectrum of the ray. Plot in
        wavelegnth (lambda) space. Not formatted to be used in spectacle fitting

        Parameters
        -----------
        ax : matplotlib axis
            axis in which to draw the spectra plot

        Returns
        --------
            wavelength: YT array
                Array of wavelength values of the generated spectra (in km/s)

            flux: YT array
                Array of the normalized flux values of the generated spectra
        """
        #set which ions to add to spectra
        ion_list = self.ion_list

        #adjust wavelegnth_center for redshift
        rest_wavelength = self.wavelength_center
        wave_min = rest_wavelength - self.wavelength_width/2
        wave_max = rest_wavelength + self.wavelength_width/2

        #use wavelength_width to set the range
        spect_gen = trident.SpectrumGenerator(lambda_min=wave_min, lambda_max=wave_max, dlambda = self.wavelegnth_res)
        spect_gen.make_spectrum(self.data, lines=ion_list, observing_redshift=self.ds.current_redshift)


        #get fields from spectra and give correct units
        rest_wavelength = rest_wavelength*u.Unit('angstrom')
        wavelength = spect_gen.lambda_field * u.Unit('angstrom')
        flux = spect_gen.flux_field

        if ax is not None:
            #plot values for spectra
            ax.plot(wavelength[:-1], flux[:-1])
            ax.set_ylim(0, 1.05)
            ax.set_xlim(wave_min, wave_max)
            ax.xaxis.set_minor_locator(AutoMinorLocator(2))
            ax.set_title(f"Spectrum {self.ion_name}", loc='right')
            ax.set_xlabel("Wavelength $\AA$")
            ax.set_ylabel("Flux")
            ax.grid(zorder=0, which='both')

        return wavelength, flux

    def plot_num_density(self, ax_num_dense, ax_prop2=None,
                         prop2_name='velocity_los', prop2_units=None,
                         plot_kwargs={}):
        """
        Plots the number density at different lengths along the ray

        Parameters
        ----------
        ax_num_dense : matplotlib axis
            axis in which to draw the number density plot

        ax_prop2: matplotlib axis, optional
            axis in which to draw the second field. if None, no plot is made
            Default: None

        prop2_name: str,optional
            Field to plot in second plot.
            Default:'velocity_los'

        prop2_units: str, optional
            The units to use in the second field.
            Defaults: None
        plot_kwargs: dict, optional
            A Dictionary of plot kwargs to be passed to the pyplot.plot function.
            Default: {}
        """
        #get list of num density  los velocity and corresponding lengths
        num_density = self.data[ion_p_num(self.ion_name)]
        prop2 = self.data[prop2_name]

        prop2_lb = None
        prop2_ub = None

        #load defaults for prop2
        if prop2_units is None:

            #check if defaults for field
            if prop2_name in default_units_dict.keys():
                prop2_units = default_units_dict[prop2_name]
                prop2 = prop2.in_units(prop2_units)

                # set default bounds
                if prop2_name in default_limits_dict.keys():
                    prop2_lb, prop2_ub = default_limits_dict[prop2_name]

            else:
                # use default of trident (genarlly in cgs units)
                prop2_units = str(prop2.units)
        else:
            # convert to specified units
            prop2 = prop2.in_units(prop2_units)

        #get length data and define x limits
        l_list = self.data['l'].in_units('kpc')
        full_l = self.uncut_data['l'].in_units('kpc')
        pad = 0.1*full_l[-1]
        xlimits = [-pad, full_l[-1] + pad]

        # check if l_list is non-empty cuz something went wrong then.
        if l_list.size == 0:
            err_file = open("error_file.txt", 'a')
            err_file.write(f"{self.ray_filename} had an l_list that was of size zero")
            err_file.close()
            return 1

        if ax_num_dense is not None:
            #make num density plots
            ax_num_dense.plot(l_list, num_density, **plot_kwargs)
            ax_num_dense.set_title(f"Number Density of {self.ion_name} Along Ray", loc='right')
            ax_num_dense.set_xlabel("Length From Start of Ray $(kpc)$")
            ax_num_dense.set_ylabel("Number Density \n$(cm^{-3})$")
            ax_num_dense.set_yscale('log')
            ax_num_dense.grid(zorder=0)

            #chech if min/max num dense was called
            if (self.num_dense_min is None and self.num_dense_max is None):
                med = np.median(num_density)
                self.num_dense_min = med*0.01
                self.num_dense_max = med*1000

            #set axes limits
            ax_num_dense.set_ylim(self.num_dense_min, self.num_dense_max)
            ax_num_dense.set_xlim(xlimits[0], xlimits[1])
            #add minor tick marks
            ax_num_dense.xaxis.set_minor_locator(AutoMinorLocator(2))

            #check if should plot spice intervals
            if self.plot_spice:
                # run spice method if not already run
                if self.num_spice is None:
                    self.get_spice_absorbers()

                #plot spice intervals
                if self.num_spice > 0:
                    for i in range(self.num_spice):
                        b, e = self.spice_intervals[i]
                        curr_lcd = self.spice_df.loc[i, 'col_dens']

                        #plot interval
                        ax_num_dense.axvspan(l_list[b], l_list[e], alpha=0.5, edgecolor='black',facecolor='tab:grey')#vspan_cmap((curr_lcd-12)/11))

                        #plot on 2nd prop if axis exists
                        if ax_prop2 is not None:
                            ax_prop2.axvspan(l_list[b], l_list[e], alpha=0.5, edgecolor='black',facecolor='tab:grey')#vspan_cmap((curr_lcd-12)/11))

                    #plot number of intervals found
                    box_props = dict(boxstyle='square', facecolor='white')
                    ax_num_dense.text(0.9, 0.85, f"{self.num_spice} feat.", transform=ax_num_dense.transAxes, bbox = box_props)

                    #take three largest absorbers and sort by position
                    max_indices = self.spice_df['col_dens'].argsort()
                    max_indices = max_indices[-3:].to_numpy()
                    max_indices.sort()

                    #plot markers from left to right
                    colors=['black', 'magenta', 'yellow']
                    for i,c in zip(max_indices, colors):
                        b, e = self.spice_intervals[i]
                        lcd = self.spice_df.loc[i, 'col_dens']
                        mid_point = (l_list[b]+l_list[e])/2

                        ax_num_dense.scatter(mid_point, 0.75*self.num_dense_max,
                                             marker='v',color=c, edgecolors='black',
                                             label=f"logN={lcd:.1f}", zorder=3)

                    ax_num_dense.legend(loc='lower left', bbox_to_anchor=(-0.015, 0.95))

        #make second plot
        if ax_prop2 is not None:
            #plot zero mark if line of sight velocity
            if ax_prop2 == 'los_velocity':
                ax_prop2.hlines(0, l_list[0], l_list[-1], linestyles='dashed',alpha=0.25, zorder=1)

            ax_prop2.plot(l_list, prop2, **plot_kwargs)

            #set title and axis labels
            ax_prop2.set_title(f"{prop2_name} Along Ray", loc='right')
            ax_prop2.set_xlabel("Length From Start of Ray $(kpc)$")
            ax_prop2.set_ylabel(f"{prop2_name} $({prop2_units})$")

            #set limits
            ax_prop2.set_ylim(prop2_lb, prop2_ub)
            ax_prop2.set_xlim(xlimits[0], xlimits[1])

            #set minor ticks and grid lines
            ax_prop2.yaxis.set_minor_locator(AutoMinorLocator(2))
            ax_prop2.xaxis.set_minor_locator(AutoMinorLocator(2))
            ax_prop2.grid(zorder=0, which='major')
            ax_prop2.grid(zorder=0, which='minor', axis='y')

        #add appropriate markers to the plot
        if self.markers and ax_prop2 is not None:
            #check if marker distances have been defined
            if self.mark_dist_arr is None:
                self.add_annotations(plot=False)

            Vys = np.zeros_like(self.mark_dist_arr) - 500
            plot_markers = {}
            plot_markers.update(self.mark_kwargs)
            ax_prop2.scatter(self.mark_dist_arr.value, Vys,zorder=3, c=self.colorscale, marker=self.marker_shape, cmap=self.marker_cmap, **plot_markers)

    def create_multi_plot(self, outfname=None, markers=True, cmap="magma"):
        """
        combines the slice plot, number density plot, and spectrum plot into
        one image.

        Parameters
        -----------
        outfname: str , optional
            the file name/path in which to save the file defaults to being unsaved.
            Default: None

        markers: bool, optional
            adds markers to slice plot and number density to aid analysis between those plots.
            Default: True

        cmap:  Colormap, optional
            the color map to use for the slice plot.
            Default: magma

        Returns
        ---------
        fig : matplotlib figure:
            figure multi_plot is drawn on
        axes : matplotlib axes
            axes the three lower plots are drawn on
        """

        if (self.slice == None):
            #create the slicePlot using the field of the ion density
            self.create_slice(cmap = cmap)

        grid = AxesGrid(self.fig, (0.,0.,0.5,0.5),
                        nrows_ncols = (1, 1),
                        axes_pad = 0.5,
                        label_mode = "L",
                        share_all = False,
                        cbar_location="right",
                        cbar_mode="each",
                        cbar_size="3%",
                        cbar_pad="0%")

        #redraw slice plot onto figure
        plot = self.slice.plots[self.slice_field]
        plot.figure = self.fig
        plot.axes = grid[0].axes
        plot.cax = grid.cbar_axes[0]

        self.slice._setup_plots()

        #set up axes and draw other plots to them
        ax1 = self.fig.add_subplot(411)
        ax2 = self.fig.add_subplot(412)
        ax3 = self.fig.add_subplot(413)

        self.plot_num_density(ax1, ax_prop2=ax2)
        self.plot_vel_space(ax=ax3)

        axes= [ax1, ax2, ax3]
        #setup positioning for the plots underneath
        strt_pos = -0.255
        ax1.set_position( [0.0, strt_pos, 0.5, 0.15] )
        ax2.set_position( [0.0, strt_pos-0.16, 0.5, 0.15] )
        ax3.set_position( [0.0, strt_pos-0.4, 0.5, 0.15] )

        #set num dense and los vel to share axis
        ax1.set_xlabel("")
        ax2.set_title("", loc='right')
        ax1.get_shared_x_axes().join(ax1, ax2)
        ax1.set_xticklabels([])
        if (outfname != None):
            self.fig.savefig(outfname, bbox_inches='tight')

        return self.fig, axes

    def zoom(self, factor):
        """
        Zoom into the slice by specified factor

        Parameters
        ----------
        factor : float
            factor by which to zoom in using yt's zoom mehtod

        """

        self.slice.zoom(factor)

    def close(self):
        """
        close all opened files
        """

        self.ds.close()
        self.ray.close()
        plt.close(self.fig)

    def _get_vel_plot_annotations(self):
        """
        computes the column density along the given ray for a given ion species.
        This is done by using spectacle if use_spectacle is True. as well as
        by summing the product of the number density for a given length by that length.
        and the SPICE method

        Returns:
            line_models : list spectacle models : Individual line models for the
                        3 largest absorbers found by spectacle
            line_text : string : a string of properly formatted col dense to
                        be added on to multi_plot
        """

        # run thw two methods if not already done
        if self.num_spectacle is None:
            # run spectacle method
            self.get_spectacle_absorbers()
        if self.num_spice is None:
            self.get_spice_absorbers()


        fit_label="Spect:"
        #check if no absorbers found
        if self.num_spectacle == 0:
            line_models = None
            fit_string = "{: <14s}{: >4s}\n".format(fit_label, '--')
        else:
            #get total column density and 3 largest lines
            tot_spect_cd, line_models = self._get_large_spectacle()
            fit_string = "{: <14s}{:04.1f}\n".format(fit_label, tot_spect_cd)

        #get sum from SPICE method
        spice_label="SPICE:"
        #check if no absorbers
        if self.num_spice == 0:
            spice_string = "{: <11s}{: >4s}\n".format(spice_label,'--')
        else:
            #find total column density for SPICE method
            cd_sum=0
            for lcd in self.spice_df['col_dens']:
                cd_sum += 10**lcd

            log_cd_sum = np.log10(cd_sum)
            spice_string = "{: <11s}{:04.1f}\n".format(spice_label,log_cd_sum)

        #get total column density along ray
        ion_field = ion_p_num(self.ion_name)
        tot_ray_cd= np.sum( self.data[ion_field].in_units('cm**-3')*self.data['dl'].in_units('cm') )
        log_tot_ray = np.log10(tot_ray_cd)
        total_string="{: <14s}{:04.1f}".format("full ray:", log_tot_ray)

        #combine strings to create "legend"
        line_text = "Tot Sums\n"+spice_string + fit_string + total_string

        return line_text, line_models

    def _get_large_spectacle(self):
        """
        Return the total column density found by spectacle and the 3 largest
        absorbers found by spectacle.
        """
        #compute total column density
        line_sum_cd = 0
        for cd in self.spectacle_df['col_dens']:
            line_sum_cd+= 10**cd
        log_tot_cd = np.log10(line_sum_cd)

        line_models = []
        indx_max = self.spectacle_df['col_dens'].argsort()
        for indx in indx_max[-3:]:
            line = self.spectacle_model.lines[indx]
            line_models.append( self.spectacle_model.with_line(line, reset=True))

        #sort lines based on delta v
        line_models.sort(key=lambda mod: mod.lines[0].delta_v.value)

        return log_tot_cd, line_models

Create's plot to easily see where absorbers are found along the light ray     both directly and through resulting spectra. Uses absorber extractor as base     class.      Parameters     ----------      ds_filename: str or YT dataset         Either Path/name of the dataset to be loaded or the dataset itself      ray_filename: str or Trident ray         Path/name of the hdf5 ray file to be loaded or the ray already loaded      ion_name: string, optional         Name of the ion to extract absorbers of and plot         Default: "H I"      cut_region_filters : list of str, optional         a list of filters defined by the way you use Cut Regions in YT      slice_field : string, optional         Field to plot in slice plot. defaults to ion_name's number density      absorber_fields : list of strings, optional         Additional ions to include in plots/Spectra, enter as list.      north_vector : array type, optional         vector used to fix the orientation of the slice plot defaults to z-axis      center_gal : array type, optional         center of galaxy in code_length. if None, then defaults to domain_center      wavelength_center : float, optional         Wavelength to center spectrum plot on. defaults to the stringest known         spectral line of ion_name. in units of Angstrom      wavelength_width :float, optional         sets the wavelength range of the spectrum plot. defaults to 300 Angstroms      velocity_width :float, optional         sets the velocity range in spectrum plot in units of km/s      wavelegnth_res :float, optional         width of wavelength bins in spectrum plot. default 0.1 Angstrom      velocity_res :float, optional         width of velocity bins in spectrum plot. default 10 km/s      use_spectacle : bool, optional         Choose whether to use spectacle fit to compute col dense      plot_spectacle: bool, optional         chooses whether individual absorption lines found by spectacle are plotted      spectacle_res : double, optional         Set minimum resolution that spectacle will attempt to fit lines to. If         None, default to velocity_res      plot_spice : bool, optional         Sets whether the intervals found by the SPICE method are plotted on the         number density plot      absorber_min: float, optional         Minimum Log Column Density that will be used to define an absorber.         If None, defaults to either default for specific ion or 13         Default: None      frac: float, optional         Parameter defining what fraction of the number density is being         accounted for in each iteration of the SPICE method. Must be a number         between 0 and 1.         Default: 0.8      num_dense_min: float, optional         Sets the lower limit for the number density plot. If None, defaults to         0.01 times the median number density      num_dense_max: float, optional         Sets the upper limit for the number density plot. If None, defaults to         100 times the median number density      markers :bool, optional         whether to include markers on light ray and number density plot      mark_plot_args : dict, optional         set the property of markers if they are to be plotted.         optional settings are:          `marker_spacing`: determines how far apart markers are in kpc.          `marker_shape`: shape of marker see matplotlib for notation          `marker_cmap`: colormap used to differentiate markers any other property that can be passer to matplotlib scatter      figure :matplotlib figure, optional         where the multi_plot will be plotted. creates one if none is specified.       Notes     ------     ion names should be in following notaion: neutral Hydrogen-->"H I",     5-times ionized Oxygen --> "O VI" #set file names and ion name #add ion name to list of all ions to be plotted #add ion fields to dataset if not already there #set a value for slice #open up the ray files #set slice field to ion name if no field is specified # whether to use/plot these methods # define defaults for spectacle fit #add user defined defaults #parameters for trident #default spectacle resolution to velocity_res #default set the wavelength center to one of the known spectral lines #for ion name. Use tridents line database to search for correct wavelength #open up tridents default line database #find all lines that match ion #take one with largest f_value #open up a figure if none specified #set marker plot properties #optionally set min/max value for number density plot Adds ray and marker annotations to slice plot          Parameters         -----------         plot : bool             Whether to annotate ray/markers to the slice plot or to just             calculate the marker positions for placing on los_velocity plot #annotate ray #get ray positional properties #make marker every x kpc. skip start #kpc #define colormap and scale #construct unit vec from ray #calculate the position #choose correct color from cmap Create a slice in the Dataset along the path of the ray.         Choose to keep the Z direction maintained.          Parameters         ----------          cmap: str             the colormap to use for the slice. Default: 'magma'          Returns         -------         slice : yt SlicePlot             Slice with ray annotated #print("adding ion fields") # runs way to slow, may add later #self.cut_region_filters is not None: # parse for radial cuts # cuts running too slow rn so just not including them #construct vec orthogonal to ray/plane #set center to domain_center unless specified #adjust center so that it is in the plane of ray and north_vector #set width/height #default to length of ray #width still defaults to length of ray #Create slice along ray. keep slice pointed in north_Vec direction #set axes to kpc #annotate plot # set color map # set background to bottom of color map Use trident to plot the absorption spectrum of the ray in velocity         space. Compute column densities with spectacle fits.          Parameters         -----------         ax: matplotlib axis object, optional             an axis in which to draw the velocity plot. If None, no plot is             not drawn.             Default: None          annotate_column_density: bool, optional             if True, add a textbox reporting the calculated col densities             by each method to the plot.             Default: True          Returns         ----------             velocity: YT array                 Array of velocity values of the generated spectra (in km/s)              flux: YT array                 Array of the normalized flux values of the generated spectra # add wav center first so it is set as zero point velocity by trident #set up spectra #generate spectra and return fields #plot values for velocity plot #annotate plot with column densities #annotate number of lines #plot individual column lines #plot centroids of largest lines #plott the largest lines Use trident to plot the absorption spectrum of the ray. Plot in         wavelegnth (lambda) space. Not formatted to be used in spectacle fitting          Parameters         -----------         ax : matplotlib axis             axis in which to draw the spectra plot          Returns         --------             wavelength: YT array                 Array of wavelength values of the generated spectra (in km/s)              flux: YT array                 Array of the normalized flux values of the generated spectra #set which ions to add to spectra #adjust wavelegnth_center for redshift #use wavelength_width to set the range #get fields from spectra and give correct units #plot values for spectra Plots the number density at different lengths along the ray          Parameters         ----------         ax_num_dense : matplotlib axis             axis in which to draw the number density plot          ax_prop2: matplotlib axis, optional             axis in which to draw the second field. if None, no plot is made             Default: None          prop2_name: str,optional             Field to plot in second plot.             Default:'velocity_los'          prop2_units: str, optional             The units to use in the second field.             Defaults: None         plot_kwargs: dict, optional             A Dictionary of plot kwargs to be passed to the pyplot.plot function.             Default: {} #get list of num density  los velocity and corresponding lengths #load defaults for prop2 #check if defaults for field # set default bounds # use default of trident (genarlly in cgs units) # convert to specified units #get length data and define x limits # check if l_list is non-empty cuz something went wrong then. #make num density plots #chech if min/max num dense was called #set axes limits #add minor tick marks #check if should plot spice intervals # run spice method if not already run #plot spice intervals #plot interval #vspan_cmap((curr_lcd-12)/11)) #plot on 2nd prop if axis exists #vspan_cmap((curr_lcd-12)/11)) #plot number of intervals found #take three largest absorbers and sort by position #plot markers from left to right #make second plot #plot zero mark if line of sight velocity #set title and axis labels #set limits #set minor ticks and grid lines #add appropriate markers to the plot #check if marker distances have been defined combines the slice plot, number density plot, and spectrum plot into         one image.          Parameters         -----------         outfname: str , optional             the file name/path in which to save the file defaults to being unsaved.             Default: None          markers: bool, optional             adds markers to slice plot and number density to aid analysis between those plots.             Default: True          cmap:  Colormap, optional             the color map to use for the slice plot.             Default: magma          Returns         ---------         fig : matplotlib figure:             figure multi_plot is drawn on         axes : matplotlib axes             axes the three lower plots are drawn on #create the slicePlot using the field of the ion density #redraw slice plot onto figure #set up axes and draw other plots to them #setup positioning for the plots underneath #set num dense and los vel to share axis Zoom into the slice by specified factor          Parameters         ----------         factor : float             factor by which to zoom in using yt's zoom mehtod close all opened files computes the column density along the given ray for a given ion species.         This is done by using spectacle if use_spectacle is True. as well as         by summing the product of the number density for a given length by that length.         and the SPICE method          Returns:             line_models : list spectacle models : Individual line models for the                         3 largest absorbers found by spectacle             line_text : string : a string of properly formatted col dense to                         be added on to multi_plot # run thw two methods if not already done # run spectacle method #check if no absorbers found #get total column density and 3 largest lines #get sum from SPICE method #check if no absorbers #find total column density for SPICE method #get total column density along ray #combine strings to create "legend" Return the total column density found by spectacle and the 3 largest         absorbers found by spectacle. #compute total column density #sort lines based on delta v