morphgen-rates 0.2.0__tar.gz → 0.3.0__tar.gz

{morphgen_rates-0.2.0/src/morphgen_rates.egg-info → morphgen_rates-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: morphgen-rates
-Version: 0.2.0
+Version: 0.3.0
 Summary: Compute bifurcation and annihilation rates from morphology data
 Author-email: Francesco Cavarretta <fcavarretta@ualr.edu>
 Requires-Python: >=3.9

{morphgen_rates-0.2.0 → morphgen_rates-0.3.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "morphgen-rates"
-version = "0.2.0"
+version = "0.3.0"
 description = "Compute bifurcation and annihilation rates from morphology data"
 authors = [
   { name = "Francesco Cavarretta", email = "fcavarretta@ualr.edu" },

{morphgen_rates-0.2.0 → morphgen_rates-0.3.0}/src/morphgen_rates/data.py

@@ -1,47 +1,8 @@
 import pandas as pd
 from pathlib import Path
 
-_file_list = {
-  'aPC':{
-    'SL':{
-      'apical':{
-        'fname_sholl':'sl_apical_sholl_plot',
-        'fname_bif':'sl_apical_bifurcations'
-        }
-      },
-    'PYR':{
-      'apical':{
-        'fname_sholl':'pyr_apical_sholl_plot',
-        'fname_bif':'pyr_apical_bifurcations'
-        }
-      },
-    },
-  'NEOC':{
-    'PYR':{
-      'apical':{
-        'fname_sholl':'neocortex_sholl_plot',
-        'fname_bif':'neocortex_bifurcations'
-        }
-      },
-    },
-  'OB':{
-    'MITRAL':{
-      'lateral':{
-        'fname_sholl':'mitral_sholl_plot',
-        'fname_bif':'mitral_bifurcations'
-        }
-      },
-    'TUFTED':{
-      'lateral':{
-        'fname_sholl':'tufted_sholl_plot',
-        'fname_bif':'tufted_bifurcations'
-        }
-      },
-    }
-  }
-
-
-def _local_data_path(filename, ext="csv"):
+
+def _local_data_path(filename='morph_data', ext="csv"):
   """
   Build a path like: <this_file_dir>/data/<filename>.<ext>
 
@@ -58,79 +19,10 @@ def _local_data_path(filename, ext="csv"):
       Full path to the data file
   """
   work_dir = Path(__file__).resolve().parent
-  return work_dir / "data" / f"{filename}.{ext}"
+  return work_dir / f"{filename}.{ext}"
 
 
-def _get_by_path(d, path, sep="/"):
-  """
-  Retrieve a value from a nested dictionary using a path-like key string.
-
-  Example
-  -------
-  d = {"a": {"b": {"c": 123}}}
-  get_by_path(d, "a/b/c") -> 123
-
-  Parameters
-  ----------
-  d : dict
-      Nested dictionary
-  path : str
-      Path of keys, e.g. "keys1/keys2/keys3"
-  sep : str, default "/"
-      Path separator
-
-  Returns
-  -------
-  object
-      The value stored at the given path
-
-  Raises
-  ------
-  KeyError
-      If any key along the path is missing
-  TypeError
-      If a non-dict is encountered before the final key
-  """
-  cur = d
-  for k in path.split(sep):
-    if not isinstance(cur, dict):
-      raise TypeError(f"Expected dict at '{k}', got {type(cur).__name__}")
-    cur = cur[k]
-  return cur
-
-
-def _get_data(fname_sholl, fname_bif):  
-  data = {}
-  
-  # Load Sholl plot summary statistics (bin counts + variance) from CSV
-  if fname_sholl:
-    df_sholl = pd.read_csv(_local_data_path(fname_sholl), index_col=0)
-    # manipulate the data
-    df_sholl = df_sholl.T.describe().T[['mean', 'std']]
-    df_sholl = df_sholl[(df_sholl != 0).all(axis=1)]
-    bin_size = df_sholl.index[1] - df_sholl.index[0]
-    df_sholl = df_sholl.to_numpy()
-
-    data['sholl'] = {
-      'bin_size':bin_size, 
-      'mean':df_sholl[:, 0],
-      'var':df_sholl[:, 1] ** 2,
-      }
-
-  if fname_bif:
-    # Load bifurcation summary statistics from CSV
-    df_bif = pd.read_csv(_local_data_path(fname_bif), index_col=0).to_numpy()
-
-    # Bundle inputs exactly as loaded (no preprocessing)
-    data["bifurcations"] = {
-      'mean':df_bif.mean(),
-      'var':df_bif.var()
-      }
-
-  return data
-
-
-def get_data(data_path):
+def get_data(key):
   """
   Retrieve a dataset entry using a key-path of the form
   "<brain region>/<neuron class>/<subcellular section>".
@@ -143,7 +35,7 @@ def get_data(data_path):
 
   Parameters
   ----------
-  data_path : str
+  key : str
       Dataset identifier expressed as a key path:
 
       "<brain region>/<neuron class>/<subcellular section>"
@@ -203,5 +95,53 @@ def get_data(data_path):
   >>> data["bifurcations"]["mean"]
   12.3
   """
-  return _get_data(**_get_by_path(_file_list, data_path))
+  data = {}
+
+  # split the key
+  parts = tuple(p.strip() for p in key.split("/") if p.strip())
+  if len(parts) != 2:
+      raise ValueError(f"Expected key like 'area/neuron_type', got: {key!r}")
+  area, neuron_type = parts
+    
+  # load data
+  df = pd.read_csv(_local_data_path(), index_col=0)
+
+  # select specific area and neuron type
+  df = df[(df['area'] == area) & (df['neuron_type'] == neuron_type)]
   
+  # neuron name unnecessary
+  df.drop(['area', 'neuron_type', 'neuron_name'], axis=1, inplace=True)
+
+  # statistics
+  df = df.groupby('section_type').describe()
+
+  # select only a subset of columns
+  df = df.loc[:, df.columns.get_level_values(1).isin(['mean', 'std', 'min', 'max'])]
+
+  # get subsections
+  for section_type, row in df.iterrows():
+    data[section_type] = {}
+
+    print()
+
+    # get statistics
+    for data_type in ['bifurcation_count', 'total_length']:
+      tmp = row.loc[row.index.get_level_values(0) == data_type, :]
+      tmp.index = tmp.index.droplevel(0)
+      data[section_type][data_type] = tmp.to_dict()
+
+    # count neurites at the soma
+    tmp = row.loc[row.index.get_level_values(0) == 'Count0', :]
+    tmp.index = tmp.index.droplevel(0)
+    data[section_type]['primary_count'] = tmp.to_dict()
+    
+    # sholl plots
+    tmp = row.loc[row.index.get_level_values(0).str.startswith('Count'), :]
+    data[section_type]['sholl_plot'] = {
+      'bin_size':row[('bin_size', 'mean')].tolist(),
+      'mean':tmp.loc[tmp.index.get_level_values(1) == 'mean', :].tolist(),
+      'std':tmp.loc[tmp.index.get_level_values(1) == 'std', :].tolist()
+      }
+
+  return data
+

{morphgen_rates-0.2.0 → morphgen_rates-0.3.0}/src/morphgen_rates/rates.py

@@ -35,23 +35,23 @@ def compute_rates(data, max_step_size):
       Input container with the following structure:
 
       data = {
-        "sholl": {
+        "sholl_plot": {
           "bin_size": float,
           "mean": numpy.ndarray,   # shape (K,)
           "var":  numpy.ndarray,   # shape (K,)
         },
-        "bifurcations": {
+        "bifurcation_count": {
           "mean": float,
           "var":  float,
         },
       }
 
       Where:
-      - `data["sholl"]["bin_size"]` is the spatial bin size used to build the Sholl plot
-      - `data["sholl"]["mean"][i]` is the mean Sholl intersection count in bin i
-      - `data["sholl"]["var"][i]` is the variance of the Sholl intersection count in bin i
-      - `data["bifurcations"]["mean"]` is the mean number of bifurcations
-      - `data["bifurcations"]["var"]` is the variance of the number of bifurcations
+      - `data["sholl_plot"]["bin_size"]` is the spatial bin size used to build the Sholl plot
+      - `data["sholl_plot"]["mean"][i]` is the mean Sholl intersection count in bin i
+      - `data["sholl_plot"]["var"][i]` is the variance of the Sholl intersection count in bin i
+      - `data["bifurcation_count"]["mean"]` is the mean number of bifurcations
+      - `data["bifurcation_count"]["var"]` is the variance of the number of bifurcations
 
     max_step_size : float
       Maximum advancement (in distance from the soma) allowed for a single
@@ -71,7 +71,7 @@ def compute_rates(data, max_step_size):
 
     Notes
     -----
-    - `data["sholl"]["mean"]` and `data["sholl"]["var"]` must be 1D arrays of equal length
+    - `data["sholl_plot"]["mean"]` and `data["sholl_plot"]["var"]` must be 1D arrays of equal length
     - Variances must be non-negative
     - Ensure `bin_size` and `max_step_size` use consistent spatial units
     """    
@@ -86,12 +86,15 @@ def compute_rates(data, max_step_size):
 
 
     global _Mean_Penalty, _Var_Penalty
-    dx = data['sholl']['bin_size']
-    Z =  data['sholl']['mean']
-    V = data['sholl']['var']
+    dx = data['sholl_plot']['bin_size']
+
+    min_zero_bin = min(data['sholl_plot']['mean'].index(0), data['sholl_plot']['std'].index(0))
+    
+    Z =  np.array(data['sholl_plot']['mean'][:min_zero_bin])
+    V = np.power(data['sholl_plot']['std'][:min_zero_bin], 2)
 
     if 'bifurcations' in data:
-        n_bif = [data['bifurcations']['mean'], data['bifurcations']['var']]
+        n_bif = [data['bifurcation_count']['mean'], data['bifurcation_count']['std'] ** 2]
     else:
         n_bif = None
 

{morphgen_rates-0.2.0 → morphgen_rates-0.3.0/src/morphgen_rates.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: morphgen-rates
-Version: 0.2.0
+Version: 0.3.0
 Summary: Compute bifurcation and annihilation rates from morphology data
 Author-email: Francesco Cavarretta <fcavarretta@ualr.edu>
 Requires-Python: >=3.9

morphgen_rates-0.3.0/src/morphgen_rates.egg-info/SOURCES.txt

@@ -0,0 +1,12 @@
+LICENSE
+README.md
+pyproject.toml
+src/morphgen_rates/__init__.py
+src/morphgen_rates/data.py
+src/morphgen_rates/rates.py
+src/morphgen_rates.egg-info/PKG-INFO
+src/morphgen_rates.egg-info/SOURCES.txt
+src/morphgen_rates.egg-info/dependency_links.txt
+src/morphgen_rates.egg-info/requires.txt
+src/morphgen_rates.egg-info/top_level.txt
+tests/test.py

{morphgen_rates-0.2.0 → morphgen_rates-0.3.0}/tests/test.py

@@ -2,7 +2,7 @@ import pandas as pd
 from morphgen_rates import compute_rates, get_data
 
 # Bundle inputs exactly as loaded (no preprocessing)
-data = get_data('aPC/PYR/apical')
+data = get_data('aPC/PYR')['apical_dendrite']
 
 print(data)
 

morphgen_rates-0.2.0/src/morphgen_rates/data/mitral_bifurcations.csv

@@ -1,10 +0,0 @@
-,0
-0,19
-1,12
-2,17
-3,13
-4,11
-5,5
-6,21
-7,22
-8,20

morphgen_rates-0.2.0/src/morphgen_rates/data/mitral_sholl_plot.csv

@@ -1,29 +0,0 @@
-Distance,Count0,Count1,Count2,Count3,Count4,Count5,Count6,Count7,Count8
-0.0,7.0,4.0,7.0,4.0,3.0,9.0,5.0,5.0,5.0
-50.0,8.0,6.0,8.0,5.0,5.0,10.0,8.0,7.0,7.0
-100.0,14.0,11.0,9.0,6.0,7.0,11.0,8.0,9.0,11.0
-150.0,16.0,14.0,14.0,8.0,8.0,11.0,11.0,13.0,12.0
-200.0,16.0,11.0,14.0,10.0,8.0,12.0,12.0,14.0,14.0
-250.0,15.0,16.0,14.0,11.0,8.0,14.0,12.0,15.0,15.0
-300.0,18.0,12.0,15.0,14.0,9.0,14.0,14.0,17.0,16.0
-350.0,17.0,14.0,15.0,12.0,9.0,13.0,12.0,18.0,18.0
-400.0,17.0,12.0,17.0,12.0,9.0,13.0,11.0,19.0,18.0
-450.0,18.0,8.0,17.0,14.0,9.0,12.0,11.0,20.0,18.0
-500.0,17.0,10.0,17.0,11.0,8.0,12.0,11.0,20.0,18.0
-550.0,16.0,8.0,13.0,11.0,7.0,11.0,9.0,18.0,17.0
-600.0,15.0,7.0,12.0,7.0,7.0,9.0,9.0,16.0,15.0
-650.0,13.0,6.0,12.0,6.0,8.0,9.0,8.0,13.0,14.0
-700.0,9.0,4.0,11.0,5.0,7.0,8.0,8.0,12.0,14.0
-750.0,10.0,4.0,11.0,3.0,7.0,5.0,6.0,10.0,13.0
-800.0,6.0,4.0,8.0,2.0,7.0,2.0,5.0,10.0,10.0
-850.0,2.0,5.0,7.0,0.0,4.0,2.0,4.0,6.0,8.0
-900.0,2.0,4.0,3.0,0.0,2.0,0.0,3.0,4.0,6.0
-950.0,2.0,3.0,3.0,0.0,2.0,0.0,2.0,2.0,4.0
-1000.0,2.0,2.0,2.0,0.0,1.0,0.0,1.0,1.0,1.0
-1050.0,2.0,2.0,0.0,0.0,0.0,0.0,2.0,1.0,0.0
-1100.0,0.0,2.0,0.0,0.0,0.0,0.0,2.0,0.0,0.0
-1150.0,0.0,1.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0
-1200.0,0.0,1.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0
-1250.0,0.0,1.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0
-1300.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0
-1350.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0

morphgen_rates-0.2.0/src/morphgen_rates/data/neocortex_apical_sholl_plot.csv

@@ -1,29 +0,0 @@
-Distance,Count0,Count1,Count2,Count3,Count4,Count5,Count6,Count7,Count8
-0.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0
-50.0,3.0,4.0,4.0,4.0,4.0,2.0,10.0,4.5,1.0
-100.0,7.0,7.0,6.0,7.0,10.0,3.0,9.0,8.0,14.0
-150.0,9.0,11.0,7.0,2.0,8.0,5.0,6.0,12.0,12.0
-200.0,4.0,6.0,8.0,12.0,9.0,9.0,6.0,18.0,8.0
-250.0,1.0,3.0,5.0,5.0,5.0,4.0,1.0,13.0,6.0
-300.0,2.0,2.0,2.0,3.0,2.0,2.0,3.0,5.0,1.0
-350.0,1.0,2.0,1.0,1.0,2.0,1.0,1.0,3.0,1.0
-400.0,1.0,2.0,1.0,1.0,2.0,2.0,1.0,1.0,1.0
-450.0,2.0,2.0,1.0,1.0,2.0,3.0,3.0,1.0,1.0
-500.0,2.0,3.0,1.0,3.0,3.0,3.0,1.0,1.0,1.0
-550.0,2.0,4.0,1.0,4.0,2.0,4.0,3.0,1.0,2.0
-600.0,4.0,4.0,1.0,5.0,3.0,4.0,3.0,1.0,4.0
-650.0,7.0,4.0,1.0,3.0,3.0,5.0,4.0,3.0,6.0
-700.0,6.0,3.0,2.0,4.0,3.0,7.0,10.0,3.0,14.0
-750.0,10.0,9.0,2.0,8.0,4.0,8.0,12.0,4.0,4.0
-800.0,0.0,17.0,2.0,10.0,4.0,10.0,1.0,4.0,0.0
-850.0,0.0,3.0,2.0,4.0,9.0,11.0,0.0,4.0,0.0
-900.0,0.0,0.0,3.0,0.0,19.0,1.0,0.0,5.0,0.0
-950.0,0.0,0.0,6.0,0.0,16.0,0.0,0.0,7.0,0.0
-1000.0,0.0,0.0,7.0,0.0,0.0,0.0,0.0,10.0,0.0
-1050.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0
-1100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-1150.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-1200.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-1250.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-1300.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
-1350.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0

morphgen_rates-0.2.0/src/morphgen_rates/data/neocortex_bifurcations.csv

@@ -1,10 +0,0 @@
-,0
-0,47
-1,119
-2,43
-3,90
-4,85
-5,65
-6,63
-7,65
-8,53

morphgen_rates-0.2.0/src/morphgen_rates/data/pyr_apical_bifurcations.csv

@@ -1,13 +0,0 @@
-,0
-0,23
-1,30
-2,18
-3,21
-4,19
-5,18
-6,17
-7,15
-8,14
-9,15
-10,15
-11,21

morphgen_rates-0.2.0/src/morphgen_rates/data/pyr_apical_sholl_plot.csv

@@ -1,17 +0,0 @@
-Distance,Count0,Count1,Count2,Count3,Count4,Count5,Count6,Count7,Count8,Count9,Count10,Count11
-0.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,2.0,1.0,1.0,1.0,1.0
-50.0,4.0,1.0,6.0,3.0,3.0,5.0,2.0,2.0,2.0,2.0,2.0,3.0
-100.0,5.0,1.0,5.0,6.0,3.0,4.0,2.0,2.0,5.0,2.0,5.0,8.0
-150.0,3.0,2.0,6.0,6.0,4.0,4.0,4.0,4.0,8.0,3.0,8.0,10.0
-200.0,5.0,4.0,6.0,7.0,5.0,5.0,6.0,6.0,10.0,5.0,7.0,15.0
-250.0,7.0,4.0,9.0,11.0,6.0,5.0,6.0,6.0,12.0,7.0,10.0,15.0
-300.0,13.0,7.0,11.0,11.0,4.0,6.0,4.0,9.0,11.0,9.0,11.0,15.0
-350.0,20.0,8.0,12.0,12.0,7.0,8.0,4.0,8.0,9.0,11.0,12.0,13.0
-400.0,11.0,8.0,11.0,8.0,7.0,6.0,4.0,12.0,1.0,12.0,14.0,3.0
-450.0,0.0,16.0,12.0,5.0,10.0,7.0,6.0,12.0,0.0,9.0,13.0,1.0
-500.0,0.0,14.0,11.0,2.0,14.0,9.0,8.0,12.0,0.0,9.0,6.0,0.0
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-600.0,0.0,10.0,7.0,0.0,8.0,6.0,3.0,4.0,0.0,1.0,0.0,0.0
-650.0,0.0,3.0,0.0,0.0,2.0,2.0,0.0,0.0,0.0,1.0,0.0,0.0
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-750.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0

morphgen_rates-0.2.0/src/morphgen_rates/data/sl_apical_bifurcations.csv

@@ -1,4 +0,0 @@
-,0
-0,24
-1,26
-2,4

morphgen_rates-0.2.0/src/morphgen_rates/data/sl_apical_sholl_plot.csv

@@ -1,11 +0,0 @@
-Distance,Count0,Count1,Count2
-0.0,2.0,2.0,1.0
-50.0,5.0,5.0,2.0
-100.0,8.0,7.0,2.0
-150.0,15.0,5.0,1.0
-200.0,16.0,8.0,1.0
-250.0,17.0,9.0,2.0
-300.0,11.0,10.0,2.0
-350.0,4.0,10.0,2.0
-400.0,0.0,1.0,2.0
-450.0,0.0,0.0,0.0

morphgen_rates-0.2.0/src/morphgen_rates/data/tufted_bifurcations.csv

@@ -1,6 +0,0 @@
-,0
-0,40
-1,21
-2,67
-3,49
-4,22

morphgen_rates-0.2.0/src/morphgen_rates/data/tufted_sholl_plot.csv

@@ -1,29 +0,0 @@
-Distance,Count0,Count1,Count2,Count3,Count4
-0.0,2.0,2.0,1.0,7.0,1.0
-50.0,4.0,12.0,3.0,8.0,8.0
-100.0,3.0,11.0,4.0,11.0,11.0
-150.0,6.0,10.0,4.0,10.0,10.0
-200.0,11.0,10.0,4.0,16.0,10.0
-250.0,10.0,10.0,21.0,17.0,8.0
-300.0,4.0,8.0,8.0,17.0,8.0
-350.0,4.0,8.0,6.0,12.0,8.0
-400.0,3.0,8.0,7.0,12.0,8.0
-450.0,3.0,7.0,8.0,11.0,7.0
-500.0,5.0,7.0,7.0,10.0,8.0
-550.0,3.0,10.0,9.0,11.0,7.0
-600.0,2.0,11.0,6.0,11.0,8.0
-650.0,2.0,7.0,2.0,12.0,5.0
-700.0,2.0,6.0,2.0,7.0,5.0
-750.0,2.0,4.0,3.0,4.0,5.0
-800.0,0.0,2.0,1.0,3.0,4.0
-850.0,0.0,1.0,1.0,1.0,1.0
-900.0,0.0,1.0,1.0,1.0,1.0
-950.0,0.0,1.0,0.0,1.0,1.0
-1000.0,0.0,1.0,0.0,0.0,0.0
-1050.0,0.0,0.0,0.0,0.0,0.0
-1100.0,0.0,0.0,0.0,0.0,0.0
-1150.0,0.0,0.0,0.0,0.0,0.0
-1200.0,0.0,0.0,0.0,0.0,0.0
-1250.0,0.0,0.0,0.0,0.0,0.0
-1300.0,0.0,0.0,0.0,0.0,0.0
-1350.0,0.0,0.0,0.0,0.0,0.0

morphgen_rates-0.2.0/src/morphgen_rates.egg-info/SOURCES.txt

@@ -1,22 +0,0 @@
-LICENSE
-README.md
-pyproject.toml
-src/morphgen_rates/__init__.py
-src/morphgen_rates/data.py
-src/morphgen_rates/rates.py
-src/morphgen_rates.egg-info/PKG-INFO
-src/morphgen_rates.egg-info/SOURCES.txt
-src/morphgen_rates.egg-info/dependency_links.txt
-src/morphgen_rates.egg-info/requires.txt
-src/morphgen_rates.egg-info/top_level.txt
-src/morphgen_rates/data/mitral_bifurcations.csv
-src/morphgen_rates/data/mitral_sholl_plot.csv
-src/morphgen_rates/data/neocortex_apical_sholl_plot.csv
-src/morphgen_rates/data/neocortex_bifurcations.csv
-src/morphgen_rates/data/pyr_apical_bifurcations.csv
-src/morphgen_rates/data/pyr_apical_sholl_plot.csv
-src/morphgen_rates/data/sl_apical_bifurcations.csv
-src/morphgen_rates/data/sl_apical_sholl_plot.csv
-src/morphgen_rates/data/tufted_bifurcations.csv
-src/morphgen_rates/data/tufted_sholl_plot.csv
-tests/test.py