Skip to content

Commit

Permalink
feat: allow info methods to save output to string buffer
Browse files Browse the repository at this point in the history
  • Loading branch information
@sanjayankur31
sanjayankur31 committed Nov 6, 2024
1 parent 7ee10d8 commit 6766192
Show file tree
Hide file tree
Showing 2 changed files with 102 additions and 55 deletions.
69 changes: 42 additions & 27 deletions neuroml/nml/helper_methods.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1302,9 +1302,8 @@ def get_segment_groups_by_substring(self, substring: str, unbranched: bool = Fal
return sgs
def summary(self, morph=True, biophys=True):
def summary(self, morph=True, biophys=True, string_buffer=None):
"""Print cell summary.
Shows the number of segments and segment groups, and information on the
biophysical properties of the cell. See the `morphinfo` and
`biophysinfo` methods for more details.
Expand All @@ -1315,24 +1314,30 @@ def summary(self, morph=True, biophys=True):
:type biophys: bool
:returns: None
"""
if string_buffer is None:
string_buffer = sys.stdout
print(f"*********** Summary ({self.id}) ************")
print("* Notes: "+str(self.notes))
print()
print(f"*********** Summary ({self.id}) ************", file=string_buffer)
print("* Notes: "+str(self.notes), file=string_buffer)
print(file=string_buffer)
if morph:
print(f"*********** Morphology summary ({self.id}) ************")
self.morphinfo()
print("*******************************************************")
print("Tip: use morphinfo(True) to see more detailed information.")
print(file=string_buffer)
print(f"*********** Morphology summary ({self.id}) ************", file=string_buffer)
self.morphinfo(string_buffer=string_buffer)
print("*******************************************************", file=string_buffer)
print(file=string_buffer)
if biophys:
print(f"*********** Biophys summary ({self.id}) ************")
self.biophysinfo()
print("*******************************************************")
print(file=string_buffer)
print(f"*********** Biophys summary ({self.id}) ************", file=string_buffer)
self.biophysinfo(string_buffer=string_buffer)
print("*******************************************************", file=string_buffer)
print(file=string_buffer)
def morphinfo(self, segment_detail=False):
def morphinfo(self, segment_detail=False, string_buffer=None):
"""Show info on morphology of the cell.
By default, since cells can have large numbers of segments and segment
groups, it only provides metrics on the total numbers. To see details,
Expand All @@ -1346,19 +1351,25 @@ def morphinfo(self, segment_detail=False):
:returns: None
"""
print("* Segments: "+str(len(self.morphology.segments)))
print("* SegmentGroups: "+str(len(self.morphology.segment_groups)))
if string_buffer is None:
string_buffer = sys.stdout
print("* Segments: "+str(len(self.morphology.segments)), file=string_buffer)
print("* SegmentGroups: "+str(len(self.morphology.segment_groups)), file=string_buffer)
if segment_detail:
for sg in self.morphology.segment_groups:
self.get_segment_group_info(sg.id)
def biophysinfo(self):
def biophysinfo(self, string_buffer=None):
"""Get information on the biophysical properties of the cell.
:returns: None
"""
if string_buffer is None:
string_buffer = sys.stdout
bp = None
mp = None
ip = None
Expand All @@ -1375,54 +1386,58 @@ def biophysinfo(self):
# check if there are any membrane properties
for prop, val in membp.items():
if len(val['members']) > 0:
print(f"* Membrane properties")
print(f"* Membrane properties", file=string_buffer)
break
for prop, val in membp.items():
ctype = val['type']
# objects
ms = val['members']
if len(ms) > 0:
print(f"\t* {ctype}:")
print(f"\t* {ctype}:", file=string_buffer)
for am in ms:
inf = am.info(show_contents=True, return_format="dict")
for p, v in inf.items():
print(f"\t\t* {p}: {v['members']}")
print(f"\t\t* {p}: {v['members']}", file=string_buffer)
print()
print(file=string_buffer)
intp = ip.info(show_contents=True, return_format="dict")
for prop, val in intp.items():
if len(val['members']) > 0:
print(f"* Intracellular properties")
print(f"* Intracellular properties", file=string_buffer)
break
for prop, val in intp.items():
ctype = val['type']
# objects
ms = val['members']
if len(ms) > 0:
print(f"\t* {ctype}:")
print(f"\t* {ctype}:", file=string_buffer)
for am in ms:
inf = am.info(show_contents=True, return_format="dict")
for p, v in inf.items():
print(f"\t\t* {p}: {v['members']}")
print(f"\t\t* {p}: {v['members']}", file=string_buffer)
print(file=string_buffer)
print()
def get_segment_group_info(self, group_id):
def get_segment_group_info(self, group_id, string_buffer=None):
"""Get information about a segment group
if string_buffer is None:
string_buffer = sys.stdout
:param group_id: id of segment group
:type group_id: int
:returns: None
"""
print(f"* Segment group: {group_id}:")
print(f"* Segment group: {group_id}:", file=string_buffer)
segs = self.get_all_segments_in_group(segment_group=group_id)
for s in segs:
sinfo = self.get_segment(s)
print(f"\t * {s} (Parent: {sinfo.parent.segments if sinfo.parent else '-'}; {self.get_actual_proximal(s)} -> {sinfo.distal})")
print(f"\t * {s} (Parent: {sinfo.parent.segments if sinfo.parent else '-'}; {self.get_actual_proximal(s)} -> {sinfo.distal})", file=string_buffer)
def add_segment(
self,
Expand Down
88 changes: 60 additions & 28 deletions neuroml/nml/nml.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
# -*- coding: utf-8 -*-

#
# Generated Wed Nov 6 11:43:32 2024 by generateDS.py version 2.44.1.
# Generated Wed Nov 6 17:39:46 2024 by generateDS.py version 2.44.1.
# Python 3.11.10 (main, Sep 9 2024, 00:00:00) [GCC 14.2.1 20240801 (Red Hat 14.2.1-1)]
#
# Command line options:
Expand Down Expand Up @@ -48857,9 +48857,8 @@ def get_segment_groups_by_substring(
)
return sgs

def summary(self, morph=True, biophys=True):
def summary(self, morph=True, biophys=True, string_buffer=None):
"""Print cell summary.

Shows the number of segments and segment groups, and information on the
biophysical properties of the cell. See the `morphinfo` and
`biophysinfo` methods for more details.
Expand All @@ -48870,23 +48869,44 @@ def summary(self, morph=True, biophys=True):
:type biophys: bool
:returns: None
"""
if string_buffer is None:
string_buffer = sys.stdout

print(f"*********** Summary ({self.id}) ************")
print("* Notes: " + str(self.notes))
print()
print(f"*********** Summary ({self.id}) ************", file=string_buffer)
print("* Notes: " + str(self.notes), file=string_buffer)
print(file=string_buffer)

if morph:
print(f"*********** Morphology summary ({self.id}) ************")
self.morphinfo()
print("*******************************************************")
print("Tip: use morphinfo(True) to see more detailed information.")
print(file=string_buffer)
print(
f"*********** Morphology summary ({self.id}) ************",
file=string_buffer,
)
self.morphinfo(string_buffer=string_buffer)
print(
"*******************************************************",
file=string_buffer,
)
print(
"Tip: use morphinfo(True) to see more detailed information.",
file=string_buffer,
)
print(file=string_buffer)

if biophys:
print(f"*********** Biophys summary ({self.id}) ************")
self.biophysinfo()
print("*******************************************************")
print(file=string_buffer)
print(
f"*********** Biophys summary ({self.id}) ************",
file=string_buffer,
)
self.biophysinfo(string_buffer=string_buffer)
print(
"*******************************************************",
file=string_buffer,
)
print(file=string_buffer)

def morphinfo(self, segment_detail=False):
def morphinfo(self, segment_detail=False, string_buffer=None):
"""Show info on morphology of the cell.
By default, since cells can have large numbers of segments and segment
groups, it only provides metrics on the total numbers. To see details,
Expand All @@ -48900,18 +48920,27 @@ def morphinfo(self, segment_detail=False):
:returns: None

"""
print("* Segments: " + str(len(self.morphology.segments)))
print("* SegmentGroups: " + str(len(self.morphology.segment_groups)))
if string_buffer is None:
string_buffer = sys.stdout

print("* Segments: " + str(len(self.morphology.segments)), file=string_buffer)
print(
"* SegmentGroups: " + str(len(self.morphology.segment_groups)),
file=string_buffer,
)

if segment_detail:
for sg in self.morphology.segment_groups:
self.get_segment_group_info(sg.id)

def biophysinfo(self):
def biophysinfo(self, string_buffer=None):
"""Get information on the biophysical properties of the cell.
:returns: None

"""
if string_buffer is None:
string_buffer = sys.stdout

bp = None
mp = None
ip = None
Expand All @@ -48928,55 +48957,58 @@ def biophysinfo(self):
# check if there are any membrane properties
for prop, val in membp.items():
if len(val["members"]) > 0:
print(f"* Membrane properties")
print(f"* Membrane properties", file=string_buffer)
break

for prop, val in membp.items():
ctype = val["type"]
# objects
ms = val["members"]
if len(ms) > 0:
print(f" * {ctype}:")
print(f" * {ctype}:", file=string_buffer)
for am in ms:
inf = am.info(show_contents=True, return_format="dict")
for p, v in inf.items():
print(f" * {p}: {v['members']}")
print(f" * {p}: {v['members']}", file=string_buffer)

print()
print(file=string_buffer)

intp = ip.info(show_contents=True, return_format="dict")
for prop, val in intp.items():
if len(val["members"]) > 0:
print(f"* Intracellular properties")
print(f"* Intracellular properties", file=string_buffer)
break

for prop, val in intp.items():
ctype = val["type"]
# objects
ms = val["members"]
if len(ms) > 0:
print(f" * {ctype}:")
print(f" * {ctype}:", file=string_buffer)
for am in ms:
inf = am.info(show_contents=True, return_format="dict")
for p, v in inf.items():
print(f" * {p}: {v['members']}")
print(f" * {p}: {v['members']}", file=string_buffer)

print()
print(file=string_buffer)

def get_segment_group_info(self, group_id):
def get_segment_group_info(self, group_id, string_buffer=None):
"""Get information about a segment group
if string_buffer is None:
string_buffer = sys.stdout

:param group_id: id of segment group
:type group_id: int
:returns: None

"""
print(f"* Segment group: {group_id}:")
print(f"* Segment group: {group_id}:", file=string_buffer)
segs = self.get_all_segments_in_group(segment_group=group_id)
for s in segs:
sinfo = self.get_segment(s)
print(
f" * {s} (Parent: {sinfo.parent.segments if sinfo.parent else '-'}; {self.get_actual_proximal(s)} -> {sinfo.distal})"
f" * {s} (Parent: {sinfo.parent.segments if sinfo.parent else '-'}; {self.get_actual_proximal(s)} -> {sinfo.distal})",
file=string_buffer,
)

def add_segment(
Expand Down

0 comments on commit 6766192

Please sign in to comment.