From 89062c46c783f8ca575a897e70ad834aa9bd45c8 Mon Sep 17 00:00:00 2001 From: Alex Williams Date: Sun, 3 Jan 2016 09:02:19 -0800 Subject: [PATCH] some useful funcs --- PyNeuronToolbox/morphology.py | 65 +++++++++++++++++++------ PyNeuronToolbox/record.py | 4 +- build/lib/PyNeuronToolbox/morphology.py | 65 +++++++++++++++++++------ build/lib/PyNeuronToolbox/record.py | 4 +- 4 files changed, 104 insertions(+), 34 deletions(-) diff --git a/PyNeuronToolbox/morphology.py b/PyNeuronToolbox/morphology.py index 082764c..898f4cf 100644 --- a/PyNeuronToolbox/morphology.py +++ b/PyNeuronToolbox/morphology.py @@ -139,7 +139,8 @@ def shapeplot(h,ax,sections=None,order=None,cvals=None,\ 'pre'= pre-order traversal of morphology } cvals = list/array with values mapped to color by cmap; useful for displaying voltage, calcium or some other state - variable across the shapeplot. + variable across the shapeplot. Setting cvals to the + string 'rand' will randomly color the compartments cmap = colormap used with cvals **kwargs passes on to matplotlib (e.g. color='r' for red lines) @@ -150,12 +151,12 @@ def shapeplot(h,ax,sections=None,order=None,cvals=None,\ # Default is to plot all sections. if sections is None: if order == 'pre': - sections = get_all_sections(h) # Get sections in "pre-order" + sections = allsec_preorder(h) # Get sections in "pre-order" else: sections = list(h.allsec()) # Determine color limits - if cvals is not None and clim is None: + if cvals is not None and cvals != 'rand' and clim is None: clim = [np.min(cvals), np.max(cvals)] # Plot each segement as a line @@ -164,12 +165,20 @@ def shapeplot(h,ax,sections=None,order=None,cvals=None,\ for sec in sections: xyz = get_section_path(h,sec) seg_paths = interpolate_jagged(xyz,sec.nseg) - for path in seg_paths: + if cvals =='rand': + col = np.random.uniform(0,1,3) + col[np.argmin(col)] = 0.0 + col[np.argmax(col)] = 1.0 + + for (j,path) in enumerate(seg_paths): line, = plt.plot(path[:,0], path[:,1], path[:,2], \ '-k',**kwargs) if cvals is not None: - col = cmap(int((cvals[i]-clim[0])*255/(clim[1]-clim[0]))) - line.set_color(col) + if cvals != 'rand': + col = cmap(int((cvals[i]-clim[0])*255/(clim[1]-clim[0]))) + line.set_color(col) + else: + line.set_color(col * (j/len(seg_paths))) lines.append(line) i += 1 @@ -215,7 +224,7 @@ def mark_locations(h,section,locs,markspec='or',**kwargs): rcum = np.append(0,np.cumsum(r)) # convert locs into lengths from the beginning of the path - if type(locs) is float: + if type(locs) is float or type(locs) is np.float64: locs = np.array([locs]) if type(locs) is list: locs = np.array(locs) @@ -232,7 +241,7 @@ def mark_locations(h,section,locs,markspec='or',**kwargs): xyz_marks[:,2], markspec, **kwargs) return line -def get_all_sections(h): +def allsec_preorder(h): """ Alternative to using h.allsec(). This returns all sections in order from the root. Traverses the topology each neuron in "pre-order" @@ -244,23 +253,30 @@ def get_all_sections(h): # has_parent returns a float... cast to bool if sref.has_parent() < 0.9: roots.append(section) - + # Build list of all sections - sections = [] + sec_list = [] for r in roots: - add_pre(h,sections,r) - return sections + add_pre(h,sec_list,r) + return sec_list -def add_pre(h,sec_list,section): +def add_pre(h,sec_list,section,order_list=None,branch_order=None): """ A helper function that traverses a neuron's morphology (or a sub-tree) of the morphology in pre-order. This is usually not necessary for the user to import. """ + sec_list.append(section) sref = h.SectionRef(sec=section) + + if branch_order is not None: + order_list.append(branch_order) + if len(sref.child) > 1: + branch_order += 1 + for next_node in sref.child: - add_pre(h,sec_list,next_node) + add_pre(h,sec_list,next_node,order_list,branch_order) def dist_between(h,seg1,seg2): """ @@ -269,4 +285,23 @@ def dist_between(h,seg1,seg2): (www.neuron.yale.edu/phpbb/viewtopic.php?f=2&t=2114) """ h.distance(0, seg1.x, sec=seg1.sec) - return h.distance(seg2.x, sec=seg2.sec) \ No newline at end of file + return h.distance(seg2.x, sec=seg2.sec) + +def branch_orders(h): + """ + Produces a list branch orders for each section (following pre-order tree + traversal) + """ + #Iterate over all sections, find roots + roots = [] + for section in h.allsec(): + sref = h.SectionRef(sec=section) + # has_parent returns a float... cast to bool + if sref.has_parent() < 0.9: + roots.append(section) + + # Build list of all sections + order_list = [] + for r in roots: + add_pre(h,[],r,order_list,0) + return order_list \ No newline at end of file diff --git a/PyNeuronToolbox/record.py b/PyNeuronToolbox/record.py index 3d5e5fb..3bcedd9 100644 --- a/PyNeuronToolbox/record.py +++ b/PyNeuronToolbox/record.py @@ -1,5 +1,5 @@ import numpy as np -from morphology import get_all_sections +from morphology import allsec_preorder def ez_record(h,var='v',sections=None,order=None,\ targ_names=None,cust_labels=None): @@ -24,7 +24,7 @@ def ez_record(h,var='v',sections=None,order=None,\ """ if sections is None: if order == 'pre': - sections = get_all_sections(h) + sections = allsec_preorder(h) else: sections = list(h.allsec()) if targ_names is not None: diff --git a/build/lib/PyNeuronToolbox/morphology.py b/build/lib/PyNeuronToolbox/morphology.py index 082764c..898f4cf 100644 --- a/build/lib/PyNeuronToolbox/morphology.py +++ b/build/lib/PyNeuronToolbox/morphology.py @@ -139,7 +139,8 @@ def shapeplot(h,ax,sections=None,order=None,cvals=None,\ 'pre'= pre-order traversal of morphology } cvals = list/array with values mapped to color by cmap; useful for displaying voltage, calcium or some other state - variable across the shapeplot. + variable across the shapeplot. Setting cvals to the + string 'rand' will randomly color the compartments cmap = colormap used with cvals **kwargs passes on to matplotlib (e.g. color='r' for red lines) @@ -150,12 +151,12 @@ def shapeplot(h,ax,sections=None,order=None,cvals=None,\ # Default is to plot all sections. if sections is None: if order == 'pre': - sections = get_all_sections(h) # Get sections in "pre-order" + sections = allsec_preorder(h) # Get sections in "pre-order" else: sections = list(h.allsec()) # Determine color limits - if cvals is not None and clim is None: + if cvals is not None and cvals != 'rand' and clim is None: clim = [np.min(cvals), np.max(cvals)] # Plot each segement as a line @@ -164,12 +165,20 @@ def shapeplot(h,ax,sections=None,order=None,cvals=None,\ for sec in sections: xyz = get_section_path(h,sec) seg_paths = interpolate_jagged(xyz,sec.nseg) - for path in seg_paths: + if cvals =='rand': + col = np.random.uniform(0,1,3) + col[np.argmin(col)] = 0.0 + col[np.argmax(col)] = 1.0 + + for (j,path) in enumerate(seg_paths): line, = plt.plot(path[:,0], path[:,1], path[:,2], \ '-k',**kwargs) if cvals is not None: - col = cmap(int((cvals[i]-clim[0])*255/(clim[1]-clim[0]))) - line.set_color(col) + if cvals != 'rand': + col = cmap(int((cvals[i]-clim[0])*255/(clim[1]-clim[0]))) + line.set_color(col) + else: + line.set_color(col * (j/len(seg_paths))) lines.append(line) i += 1 @@ -215,7 +224,7 @@ def mark_locations(h,section,locs,markspec='or',**kwargs): rcum = np.append(0,np.cumsum(r)) # convert locs into lengths from the beginning of the path - if type(locs) is float: + if type(locs) is float or type(locs) is np.float64: locs = np.array([locs]) if type(locs) is list: locs = np.array(locs) @@ -232,7 +241,7 @@ def mark_locations(h,section,locs,markspec='or',**kwargs): xyz_marks[:,2], markspec, **kwargs) return line -def get_all_sections(h): +def allsec_preorder(h): """ Alternative to using h.allsec(). This returns all sections in order from the root. Traverses the topology each neuron in "pre-order" @@ -244,23 +253,30 @@ def get_all_sections(h): # has_parent returns a float... cast to bool if sref.has_parent() < 0.9: roots.append(section) - + # Build list of all sections - sections = [] + sec_list = [] for r in roots: - add_pre(h,sections,r) - return sections + add_pre(h,sec_list,r) + return sec_list -def add_pre(h,sec_list,section): +def add_pre(h,sec_list,section,order_list=None,branch_order=None): """ A helper function that traverses a neuron's morphology (or a sub-tree) of the morphology in pre-order. This is usually not necessary for the user to import. """ + sec_list.append(section) sref = h.SectionRef(sec=section) + + if branch_order is not None: + order_list.append(branch_order) + if len(sref.child) > 1: + branch_order += 1 + for next_node in sref.child: - add_pre(h,sec_list,next_node) + add_pre(h,sec_list,next_node,order_list,branch_order) def dist_between(h,seg1,seg2): """ @@ -269,4 +285,23 @@ def dist_between(h,seg1,seg2): (www.neuron.yale.edu/phpbb/viewtopic.php?f=2&t=2114) """ h.distance(0, seg1.x, sec=seg1.sec) - return h.distance(seg2.x, sec=seg2.sec) \ No newline at end of file + return h.distance(seg2.x, sec=seg2.sec) + +def branch_orders(h): + """ + Produces a list branch orders for each section (following pre-order tree + traversal) + """ + #Iterate over all sections, find roots + roots = [] + for section in h.allsec(): + sref = h.SectionRef(sec=section) + # has_parent returns a float... cast to bool + if sref.has_parent() < 0.9: + roots.append(section) + + # Build list of all sections + order_list = [] + for r in roots: + add_pre(h,[],r,order_list,0) + return order_list \ No newline at end of file diff --git a/build/lib/PyNeuronToolbox/record.py b/build/lib/PyNeuronToolbox/record.py index 3d5e5fb..3bcedd9 100644 --- a/build/lib/PyNeuronToolbox/record.py +++ b/build/lib/PyNeuronToolbox/record.py @@ -1,5 +1,5 @@ import numpy as np -from morphology import get_all_sections +from morphology import allsec_preorder def ez_record(h,var='v',sections=None,order=None,\ targ_names=None,cust_labels=None): @@ -24,7 +24,7 @@ def ez_record(h,var='v',sections=None,order=None,\ """ if sections is None: if order == 'pre': - sections = get_all_sections(h) + sections = allsec_preorder(h) else: sections = list(h.allsec()) if targ_names is not None: