def array2D_to_array_list(array,axis=1):
#array: 2D array to split up into list of arrays
#axis: axis to split perpendicular to
other_axis=(axis+1)%2
if type(arraylist_rank(array)) is list:
if all(r == 1 for r in arraylist_rank(array)):
return array
else:
print "array2D_to_array_list: warning: array is already list, but arrays have rank>1"
return array
elif arraylist_rank(array) == 1:
return [array]
elif arraylist_rank(array) == 2:
return [numpy.take(array,i,axis=axis) for i in range(len(numpy.take(array,0,axis=other_axis)))]
else:
print "array2D_to_array_list: warning: arrays of rank>2 not supported"
def nstack(array,axis,n):
rank=arraylist_rank(array)
if (axis > rank):
print "nstack: warning: cannot add axis beyond the final position of the input array. Will add an axis to the final position"
axis=rank
arrays=(numpy.expand_dims(array,axis=axis),)*n
return numpy.concatenate(arrays,axis=axis)
def __init__(self,data,x,subplot_coordinates,dimensions=None,y=None,**kwargs):
#this object contains instructions for what to plot in a numpy subplot with gridspec
#dimensions: whether to visualize data as a 2D colormap, or several 1D plots in the same subplot
# this can be partially infered from the dimensions of the data
#data: the data to go into this plot. Should be a 1D, list of 1D, or 2D numpy array
#x,y: x/y grid points corresponding to the indices in the data array. y value needed for 2D arrays
#subplot_coordinates: where to put this plot on the gridspec
#**kwargs: extra visualization options that will be different depending on "dimensions".
#data_<X>axis: how to intepret the axes of the data array. <X>=x,(line),(y)
#x_<X>axis: how to intepret the axes of the x array. <X>=x,(line),(y)
#show_<X>axis: whether to show axis when plotting. <X>=x,y,(z)
#show_<X>axis_label: whether to show axis label when plotting. <X>=x,y,(z)
#kwargs that may change how we intepret the data
data_xaxis=kwarg_default("data_xaxis",0,**kwargs)
data_otheraxis=(data_xaxis+1)%2
#use rank of input data to try to determine dimensions
#and reshape appropriately
rank=arraylist_rank(data)
if rank == 1:
#put it in a list for consistency with multi-array code
data=[data]
if dimensions==None:
dimensions=1
elif rank == 2:
#can be a 2D function or several 1D.
#please manually specify to avoid ambiguity
#default assumes second index reperesents species/simulation
#if it is under or equal to 4.#
if dimensions==None:
print "perfect_subplot: warning: ambigious array rank."
if y == None:
dimensions=1
else:
dimensions=2
elif type(rank) is list:
if all(x == 1 for x in rank):
if dimensions==None:
dimensions=1
else:
print rank
print "perfect_subplot: error: input list has array(s) of rank above 1."
exit(1)
#kwargs related to tagging this subplot
self.groups=kwarg_default("groups",[],**kwargs)
#kwargs related to flagging how the subplot should be visualized
self.border_color=kwarg_default("border_color",'k',**kwargs)
self.border_linestyle=kwarg_default("border_linestyle",'solid',**kwargs)
self.title=kwarg_default("title","",**kwargs)
#axis propert kwargs
self.show_xaxis=kwarg_default("show_xaxis",True,**kwargs)
self.show_yaxis=kwarg_default("show_yaxis",True,**kwargs)
#powerlimit should be a tuple: (-a,b)
self.xaxis_powerlimits=kwarg_default("xaxis_powerlimits",None,**kwargs)
self.yaxis_powerlimits=kwarg_default("yaxis_powerlimits",None,**kwargs)
self.xaxis_label=kwarg_default("xaxis_label",None,**kwargs)
self.yaxis_label=kwarg_default("yaxis_label",None,**kwargs)
self.show_xaxis_ticklabel=kwarg_default("show_xaxis_ticklabel",False,**kwargs)
self.show_yaxis_ticklabel=kwarg_default("show_yaxis_ticklabel",False,**kwargs)
self.xscale=kwarg_default("xscale",'linear',**kwargs)
self.yscale=kwarg_default("yscale",'linear',**kwargs)
self.xlims=kwarg_default("xlims",None,**kwargs)
self.ylims=kwarg_default("ylims",None,**kwargs)
self.vlines=kwarg_default("vlines",None,**kwargs)
self.hlines=kwarg_default("hlines",None,**kwargs)
self.yaxis_label_x=kwarg_default("yaxis_label_x",-0.15,**kwargs)
self.yaxis_label_y=kwarg_default("yaxis_label_y",0.5,**kwargs)
#############################################################################
#
# 1D
#
#############################################################################
if dimensions==1:
#going to visualize 1D data
self.dimensions=1
#split 2D array into list of 1D arrays
self.data=array2D_to_array_list(data,data_otheraxis)
#print self.data
#terminology suitable for 1D case
data_lineaxis=data_otheraxis
#kwarg needed to intepret x, which can be a list of arrays here
x_xaxis=kwarg_default("x_xaxis",0,**kwargs)
x_lineaxis=(x_xaxis+1)%2
if type(arraylist_rank(x)) is not list:
if arraylist_rank(x) == 1:
if all(len(x) != len(self.data[i]) for i in range(len(self.data))):
print "perfect_subplot: 1D: error: data and x have different dimensions"
exit(1)
else:
#make the x list the same size as the data list
self.x=[x]*len(self.data)
elif arraylist_rank(x) == 2:
self.x=array2D_to_array_list(x,x_lineaxis)
else:
print "perfect_subplot: 1D: error: x has too high rank to be plotted"
exit(1)
else:
if all(len(x[i]) != len(self.data[i]) for i in range(len(self.data))):
print "perfect_subplot: 1D: error: data and x have different dimensions"
exit(1)
else:
self.x=x
#x is now a list of 1D arrays. Check compatiblity with data
if len(self.x) != len(self.data):
print "perfect_subplot: 1D: error: data and x list have different lengths"
exit(1)
elif not all(len(self.x[i]) == len(self.data[i]) for i in range(len(self.data))):
print "perfect_subplot: 1D: error: some data and x have different lengths"
exit(1)
self.subplot_coordinates=subplot_coordinates
#aesthetic kwargs
self.xticks=kwarg_default("xticks",6,**kwargs)
if self.yscale=='linear':
self.yticks=kwarg_default("yticks",5,**kwargs)
if self.yscale=='log':
self.yticks=kwarg_default("yticks",4,**kwargs)
self.hidden_xticklabels=kwarg_default("hidden_xticklabels",[],**kwargs)
self.hidden_yticklabels=kwarg_default("hidden_yticklabels",[0,-1],**kwargs)
self.linestyles=kwarg_default("linestyles",["solid"]*len(x),**kwargs)
self.markers=kwarg_default("markers",[""]*len(x),**kwargs)
self.fillstyles=kwarg_default("fillstyles",["full"]*len(x),**kwargs)
self.linewidths=kwarg_default("linewidths",[1]*len(x),**kwargs)
self.colors=kwarg_default("colors",["k"]*len(x),**kwargs)
#title position
self.title_y=kwarg_default("title_y",0.4,**kwargs)
self.title_x=kwarg_default("title_x",1.04,**kwargs)
#############################################################################
#
# 2D
#
#############################################################################
if dimensions==2:
#going to visualize 2D data
self.dimensions=2
if y is None:
print "perfect_subplot: 2D: error: need y for 2D plot."
exit(1)
#terminology suitable for 2D case
data_yaxis=data_otheraxis
if (data_xaxis == 0) and (data_yaxis == 1):
self.data=data
elif (data_xaxis == 1) and (data_yaxis == 0):
#we always want our x data along the first axis
self.data=numpy.transpose(data)
else:
print "perfect_subplot: 2D: error: data has too high rank to be plotted"
exit(1)
if (arraylist_rank(x) !=1) or (arraylist_rank(y) != 1):
print "perfect_subplot: 2D: error: x and y should have rank 1"
self.x=x
self.y=y
self.subplot_coordinates=subplot_coordinates
#kwargs related to flagging how the subplot should be visualized
#z-axis refers to the colorbar for the colormap
self.show_zaxis=kwarg_default("show_zaxis",True,**kwargs)
self.zaxis_label=kwarg_default("zaxis_label",None,**kwargs)
self.show_zaxis_ticklabel=kwarg_default("show_zaxis_ticklabel",False,**kwargs)
self.zscale=kwarg_default("zscale",'linear',**kwargs)
self.xticks=kwarg_default("xticks",4,**kwargs)
self.yticks=kwarg_default("yticks",4,**kwargs)
self.zticks=kwarg_default("zticks",4,**kwargs)
self.zlims=kwarg_default("zlims",None,**kwargs)
self.cm=kwarg_default("cm",invert_cm(cm_remove_middle(cm.RdBu,cut_radius=0.1)),**kwargs)
#self.cm=kwarg_default("cm",invert_cm(cm.RdBu),**kwargs)
#self.cm=kwarg_default("cm",diverging_rb_cm(),**kwargs)
self.symmetrize_cm=kwarg_default("symmetrize_cm",True,**kwargs)
self.hidden_xticklabels=kwarg_default("hidden_xticklabels",[0,-1],**kwargs)
self.hidden_yticklabels=kwarg_default("hidden_yticklabels",[],**kwargs)
self.hidden_zticklabels=kwarg_default("hidden_zticklabels",[],**kwargs)
#title position
self.title_y=kwarg_default("title_y",1.19,**kwargs)
self.title_x=kwarg_default("title_x",0.5,**kwargs)
