dendrotweaks 0.4.4__py3-none-any.whl → 0.4.6__py3-none-any.whl

dendrotweaks/utils.py

@@ -26,24 +26,41 @@ SWC_ID_TO_DOMAIN = {
     8: 'reduced',
 }
 
+POPULATIONS = {'AMPA': {}, 'NMDA': {}, 'AMPA_NMDA': {}, 'GABAa': {}}
+
+INDEPENDENT_PARAMS = {
+    'cm': 1, # uF/cm2
+    'Ra': 100, # Ohm cm
+    'ena': 50, # mV
+    'ek': -77, # mV
+    'eca': 140 # mV
+}
+
+DOMAIN_TO_GROUP = {
+    'soma': 'somatic',
+    'axon': 'axonal',
+    'dend': 'dendritic',
+    'apic': 'apical',
+}
+
 DOMAIN_TO_SWC_ID = {
     v: k for k, v in SWC_ID_TO_DOMAIN.items()
 }
 
-def get_swc_idx(domain_name):
-    base_domain, _, idx = domain_name.partition('_')
-    if base_domain == 'reduced':
-        return int(f'8{idx}')
-    elif base_domain == 'custom':
-        return int(f'5{idx}')
-    return DOMAIN_TO_SWC_ID.get(base_domain, 0)
-
-def get_domain_name(swc_idx):
-    if str(swc_idx).startswith('8'):
-        return 'reduced_' + str(swc_idx)[1:]
-    elif str(swc_idx).startswith('5'):
-        return 'custom_' + str(swc_idx)[1:]
-    return SWC_ID_TO_DOMAIN.get(swc_idx, 'undefined')
+DOMAINS_TO_NEURON = {
+    'soma': 'soma',
+    'perisomatic': 'dend_11',
+    'axon': 'axon',
+    'apic': 'apic',
+    'dend': 'dend',
+    'basal': 'dend_31',
+    'trunk': 'dend_41',
+    'tuft': 'dend_42',
+    'oblique': 'dend_43',
+    'custom': 'dend_5',
+    'reduced': 'dend_8',
+    'undefined': 'dend_0',
+}
 
 DOMAINS_TO_COLORS = {
     'soma': '#E69F00',
@@ -60,11 +77,24 @@ DOMAINS_TO_COLORS = {
     'undefined': '#7F7F7F',
 }
 
-def get_domain_color(domain_name):
+def get_swc_idx(domain_name):
     base_domain, _, idx = domain_name.partition('_')
-    return DOMAINS_TO_COLORS.get(base_domain, '#7F7F7F')
+    if base_domain == 'reduced':
+        return int(f'8{idx}')
+    elif base_domain == 'custom':
+        return int(f'5{idx}')
+    return DOMAIN_TO_SWC_ID.get(base_domain, 0)
 
+def get_domain_name(swc_idx):
+    if str(swc_idx).startswith('8'):
+        return 'reduced_' + str(swc_idx)[1:]
+    elif str(swc_idx).startswith('5'):
+        return 'custom_' + str(swc_idx)[1:]
+    return SWC_ID_TO_DOMAIN.get(swc_idx, 'undefined')
 
+def get_domain_color(domain_name):
+    base_domain, _, idx = domain_name.partition('_')
+    return DOMAINS_TO_COLORS.get(base_domain, '#7F7F7F')
 
 def timeit(func):
     def wrapper(*args, **kwargs):
@@ -75,7 +105,6 @@ def timeit(func):
         return result
     return wrapper
 
-
 def calculate_lambda_f(distances, diameters, Ra=35.4, Cm=1, frequency=100):
     """
     Calculate the frequency-dependent length constant (lambda_f) according to NEURON's implementation,
@@ -118,10 +147,6 @@ def calculate_lambda_f(distances, diameters, Ra=35.4, Cm=1, frequency=100):
     # Return section_L/lam (electrotonic length of the section)
     return section_L / lam
 
-if (__name__ == '__main__'):
-    print('Executing as standalone script')
-
-
 def dynamic_import(module_name, class_name):
     """
     Dynamically import a class from a module.
@@ -142,20 +167,17 @@ def dynamic_import(module_name, class_name):
     module = import_module(module_name)
     return getattr(module, class_name)
 
-
 def list_folders(path_to_folder):
     folders = [f for f in os.listdir(path_to_folder)
             if os.path.isdir(os.path.join(path_to_folder, f))]
     sorted_folders = sorted(folders, key=lambda x: x.lower())
     return sorted_folders
 
-    
 def list_files(path_to_folder, extension):
     files = [f for f in os.listdir(path_to_folder)
             if f.endswith(extension)]
     return files
 
-
 def write_file(content: str, path_to_file: str, verbose: bool = True) -> None:
     """
     Write content to a file.
@@ -175,38 +197,59 @@ def write_file(content: str, path_to_file: str, verbose: bool = True) -> None:
         f.write(content)
     print(f"Saved content to {path_to_file}")
 
-
 def read_file(path_to_file):
     with open(path_to_file, 'r') as f:
         content = f.read()
     return content
 
-
-def download_example_data(path_to_destination):
+def download_example_data(path_to_destination, include_templates=True, include_modfiles=True):
     """
-    Download the examples subfolder from the DendroTweaks GitHub repository.
+    Download and extract specific folders from the DendroTweaks GitHub repository:
+    - examples/                <- from examples subfolder (always included)
+    - examples/Templates/      <- from src/dendrotweaks/biophys/default_templates (optional)
+    - examples/Default/        <- from src/dendrotweaks/biophys/default_mod (optional)
 
     Parameters
     ----------
     path_to_destination : str
-        The path to the destination folder where the examples will be downloaded.
+        The path to the destination folder where the data will be downloaded and extracted.
+
+    include_templates : bool, optional
+        If True, also extract default_templates/ into examples/Templates/.
+
+    include_modfiles : bool, optional
+        If True, also extract default_mod/ into examples/Default/.
     """
     if not os.path.exists(path_to_destination):
         os.makedirs(path_to_destination)
 
     repo_url = "https://github.com/Poirazi-Lab/DendroTweaks/archive/refs/heads/main.zip"
-    zip_path = os.path.join(path_to_destination, "examples.zip")
+    zip_path = os.path.join(path_to_destination, "dendrotweaks_repo.zip")
 
-    print(f"Downloading examples from {repo_url}...")
+    print(f"Downloading data from {repo_url}...")
     urllib.request.urlretrieve(repo_url, zip_path)
 
-    print(f"Extracting examples to {path_to_destination}")
+    print(f"Extracting relevant folders to {path_to_destination}...")
     with zipfile.ZipFile(zip_path, 'r') as zip_ref:
         for member in zip_ref.namelist():
+            target_path = None
+
+            # === Always extract examples/ folder ===
             if member.startswith("DendroTweaks-main/examples/"):
-                # Extract the file with the correct path
-                member_path = os.path.relpath(member, "DendroTweaks-main/examples")
-                target_path = os.path.join(path_to_destination, member_path)
+                rel_path = os.path.relpath(member, "DendroTweaks-main/examples")
+                target_path = os.path.join(path_to_destination, rel_path)
+
+            # === Optionally extract Templates/ folder ===
+            elif include_templates and member.startswith("DendroTweaks-main/src/dendrotweaks/biophys/default_templates/"):
+                rel_path = os.path.relpath(member, "DendroTweaks-main/src/dendrotweaks/biophys/default_templates")
+                target_path = os.path.join(path_to_destination, "Templates", rel_path)
+
+            # === Optionally extract Default/ folder ===
+            elif include_modfiles and member.startswith("DendroTweaks-main/src/dendrotweaks/biophys/default_mod/"):
+                rel_path = os.path.relpath(member, "DendroTweaks-main/src/dendrotweaks/biophys/default_mod")
+                target_path = os.path.join(path_to_destination, "Default", rel_path)
+
+            if target_path:
                 if member.endswith('/'):
                     os.makedirs(target_path, exist_ok=True)
                 else:
@@ -214,10 +257,8 @@ def download_example_data(path_to_destination):
                     with zip_ref.open(member) as source, open(target_path, 'wb') as target:
                         target.write(source.read())
 
-    os.remove(zip_path)  # Clean up the zip file
-    print(f"Examples downloaded successfully to {path_to_destination}/.")
-
-
+    os.remove(zip_path)
+    print(f"Data downloaded and extracted successfully to {path_to_destination}/.")
 
 def apply_dark_theme():
     """
@@ -236,4 +277,71 @@ def apply_dark_theme():
         'ytick.color': 'white',
         'text.color': 'white',
         'axes.prop_cycle': plt.cycler(color=plt.cm.tab10.colors),  # use standard matplotlib colors
-    })
+    })
+
+def mse(y_true, y_pred):
+            return np.mean((np.array(y_true) - np.array(y_pred)) ** 2)
+
+def poly_fit(x, y, max_degree=6, tolerance=1e-6):
+    """
+    Fit a polynomial to the data and return the coefficients and predicted values.
+    """
+    for degree in range(max_degree + 1):
+        coeffs = np.polyfit(x, y, degree)
+        y_pred = np.polyval(coeffs, x)
+        if np.all(np.abs(np.array(y) - y_pred) < tolerance):
+            break
+    return coeffs, y_pred
+
+def step_fit(x, y):
+    """
+    Fit a single step function with variable-width transition zone.
+    Returns (high_val, low_val, start, end), and predicted y-values.
+    """
+    x = np.array(x)
+    y = np.array(y)
+
+    sort_idx = np.argsort(x)
+    x = x[sort_idx]
+    y = y[sort_idx]
+
+    best_mse = float('inf')
+    best_params = None
+    best_pred = None
+
+    n = len(x)
+    for i in range(n - 1):
+        for j in range(i + 1, n):
+            start = x[i]
+            end = x[j]
+            inside = (x > start) & (x < end)
+            outside = ~inside
+
+            if not np.any(inside) or not np.any(outside):
+                continue
+
+            high_val = np.nanmean(y[inside])
+            low_val = np.nanmean(y[outside])
+
+            pred = np.where(inside, high_val, low_val)
+            score = mse(y, pred)
+
+            if score < best_mse:
+                best_mse = score
+                best_params = (start, end, low_val, high_val)
+                best_pred = pred
+
+    return best_params, best_pred
+
+DEFAULT_FIT_MODELS = {
+    'poly': {
+        'fit': poly_fit,
+        'score': mse,
+        'complexity': lambda coeffs: len(coeffs) - 1  # degree of polynomial
+    },
+    'step': {
+        'fit': step_fit,
+        'score': mse,
+        'complexity': lambda params: 4
+    }
+}

{dendrotweaks-0.4.4.dist-info → dendrotweaks-0.4.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dendrotweaks
-Version: 0.4.4
+Version: 0.4.6
 Summary: A toolbox for exploring dendritic dynamics
 Home-page: https://dendrotweaks.dendrites.gr
 Author: Roman Makarov

{dendrotweaks-0.4.4.dist-info → dendrotweaks-0.4.6.dist-info}/RECORD

@@ -1,32 +1,35 @@
-dendrotweaks/__init__.py,sha256=Z2JpwnO9nBPrkR1w0u_6gWnCJetIhTx_27PehYlfTRM,384
-dendrotweaks/model.py,sha256=IjmLrp-Ooh1WLdTb7Xg_9q2KUO7Xuokll26NQyVITlk,70965
-dendrotweaks/model_io.py,sha256=xwXKMcUle-Y0HoWFYVZu3G8v4pdQXmeaDfl2Xi65eHw,2137
-dendrotweaks/path_manager.py,sha256=dai5o6UA0nk-ubwKWRu4LFdDBO77zW_SsMf6k0MLBiI,8703
+dendrotweaks/__init__.py,sha256=Dnklmfnnm_8cpcM-cKp-DUOhwFhG3wYFg9FGNORWbqg,384
+dendrotweaks/model.py,sha256=nj_VjIRCK2z6wx-V-hUS4KDIuYkbg9wUrk-ux8twghA,38351
+dendrotweaks/model_io.py,sha256=qY9qBs3bxsuvQSokPH_JUpT71KpYbIiLyjIDavTLtzA,27562
+dendrotweaks/model_simulation.py,sha256=sXYWTgbBOWy0dZfxjmqc_YsOgfn5y5oAfGzLsUK6u9k,9958
+dendrotweaks/path_manager.py,sha256=Bij2MMHqaBL-s9ckG0Nie5j735DTgApHRx3-ETMxUmA,8783
+dendrotweaks/prerun.py,sha256=aMNe4xh14gztkw4oCAuiJEBIgckke9oNL8vQjOEQf8s,2451
 dendrotweaks/simulators.py,sha256=OscZ4H6z9YiNloDtMAgpPx9n2e-9WJyLEWtcSD1YZR8,7411
-dendrotweaks/utils.py,sha256=jaUJNb39Bsevg3WJByP56bO7CLj1wzlh-uGZl-lxi1I,7131
-dendrotweaks/analysis/__init__.py,sha256=SEYpoQ5iXiQXyHB20-IAdDHYI-7CR5GYFXIwr-O05Ug,858
-dendrotweaks/analysis/ephys_analysis.py,sha256=PqT3aBCuxQbvdm9jnXjlTJ3R5n7_Vwp4fLrHGgtfoWw,14362
+dendrotweaks/utils.py,sha256=bZnxiQAUuc1BufBO7f3J2KGvyFCKQMDSFpfrM8_bVEo,10782
+dendrotweaks/analysis/__init__.py,sha256=tDi4BHtW1fX5iiZVk1OM3gmLo69VFmUN8AEK_F8tDq4,927
+dendrotweaks/analysis/ephys_analysis.py,sha256=v-T6IxQ48IoK6eEYcyImi9KoFrzAQU5n8k6kFyEAivc,17389
 dendrotweaks/analysis/morphometric_analysis.py,sha256=5zohjGssyx-wezI-yY3Q-kYM_wzAQLLFBJ9Xk950_JY,3571
 dendrotweaks/biophys/__init__.py,sha256=k0o2xwyoaJUb1lfO9OHtqxheNP6R-Ya5o0g-bJOdCZg,360
-dendrotweaks/biophys/distributions.py,sha256=XGczxBYJ0-vkIfXbfzvlIqlH9OpBuT9J95Kzyd2zL5A,10325
+dendrotweaks/biophys/distributions.py,sha256=m3BHHQ-iHrRLQuimIHMY4NdJCTC9cc3JT2KvLaxn28M,10324
 dendrotweaks/biophys/groups.py,sha256=Q4kBIqL1-piIgrpsVq6ojinAWHiEJ1GzMjSAQ7Ni_E8,3212
-dendrotweaks/biophys/mechanisms.py,sha256=IxKcyYftEbupJWPqGAV20Ox5a3uPbnXs3gYSlC3z-E0,18520
+dendrotweaks/biophys/mechanisms.py,sha256=ZlLTMLY53fmxwIfjEcN6Gg6S82SHXYY3EuLqiY6bGgg,18771
 dendrotweaks/biophys/default_mod/AMPA.mod,sha256=HY_pWzYvaSDV-w7qruenG2mnll8v79s40HFHjUCIi4U,980
 dendrotweaks/biophys/default_mod/AMPA_NMDA.mod,sha256=ztv2ePUiEQZ93-23FTkGO2DC91rehQuqo0NUIbHZ368,2318
 dendrotweaks/biophys/default_mod/CaDyn.mod,sha256=gwc69K_rxu2w_mV7CnOSOnVaCMc8Z-MfdBFf6lAj4kg,1298
 dendrotweaks/biophys/default_mod/GABAa.mod,sha256=jdGRid-Wzw4y9kHvq74oSMogLhSiS-Ac2DDaLOrxVi8,983
 dendrotweaks/biophys/default_mod/Leak.mod,sha256=u0lwMYGgl5kNZN5W4N6YHgRSeVxb-z2oM9fqou5rCV8,420
 dendrotweaks/biophys/default_mod/NMDA.mod,sha256=tT4Q5UPoeztXcQ45uZc2PUO3-8OkDLCmrS7WDsn1yQQ,1185
-dendrotweaks/biophys/default_mod/vecstim.mod,sha256=iSpJgR96O2Z3pLNUFIsZ7YJ529ncKUBaZqDJvA0_oV0,965
+dendrotweaks/biophys/default_mod/vecstim.mod,sha256=dcDzI3H_WeB-bO9b3NQuF16CtCaUMymPrTayZGVwRhM,826
 dendrotweaks/biophys/default_templates/NEURON_template.py,sha256=MWSv2fLKGJxdt2zfSO0b74peuBC8U9j_S6AwM5URXts,14945
 dendrotweaks/biophys/default_templates/default.py,sha256=7HEbR2GJEOhgiox1QtZUEuHi5ihNAHDLsXQiQk980tI,2201
+dendrotweaks/biophys/default_templates/jaxley.py,sha256=RFmWyLOwa0GCjkuaT-gBbjVrniu99DD3PPAs3J9os3E,4599
 dendrotweaks/biophys/default_templates/standard_channel.mod,sha256=sw80c-JyqfXNA7c7v7pZGLY-0MgFUvd3bPvJcAGXNSk,2923
 dendrotweaks/biophys/default_templates/template_jaxley.py,sha256=t-GsCSUyQ7rDoaLmyuWd9bIxB8W3bCqJdnikD59EVvI,3676
 dendrotweaks/biophys/default_templates/template_jaxley_new.py,sha256=I62KhnOYNV1bT-nPsDTxjIISYmDcso2X8rnsos28nYs,3631
 dendrotweaks/biophys/io/__init__.py,sha256=kkmQ4L0SatI3lWd3qE8KqOIKd7x3G2OnqAAW93sWWCU,575
 dendrotweaks/biophys/io/ast.py,sha256=7x_Kxz1qoQHZeIjovUNyVuKgUo4vAFKm-bd4hn9n1CI,6078
 dendrotweaks/biophys/io/code_generators.py,sha256=RX0nw5-0CyWR3KOrTZUabKuPAQg2ysQ_nQi2iu9TxiE,11978
-dendrotweaks/biophys/io/converter.py,sha256=5yrPJhyZbuwV7tTGoacnNOvmRdVgXPIyGfiR0PyOVzg,3371
+dendrotweaks/biophys/io/converter.py,sha256=-BfVFahiwlPLfM7MQiuSS8CyfZ5-PDtAHzya8a8dr3k,3567
 dendrotweaks/biophys/io/factories.py,sha256=j1Hi2u-NTFFL8ElRYlgGVNHRcfKWH6o5GfKvraMTlwM,5020
 dendrotweaks/biophys/io/grammar.py,sha256=TJLTDlr8Ajp3J9DJ4IvulOCcpUkYr7HnoI0TGnNuEPc,11677
 dendrotweaks/biophys/io/loader.py,sha256=Wv9ZkEDyA3MkCdV0sMeRnBffg2WAI7yTV3r6C412GiY,6378
@@ -34,13 +37,13 @@ dendrotweaks/biophys/io/parser.py,sha256=boT27lFrn5LYrJnkZFs0SwrZZrkSkwO8efqGPJ4
 dendrotweaks/biophys/io/reader.py,sha256=JWm5WM9illvSfDkhWEmWBcj8Y7PSi8zeZX9j1ARUHVU,6576
 dendrotweaks/morphology/__init__.py,sha256=JwXmSmdn9e_jqslITEdiU9kWvzxcxT9Aw_kUkXLbm5o,353
 dendrotweaks/morphology/domains.py,sha256=l57KVR5eo1LlH_fCd1AOMiG_SsYLBPBTGQ5R78BHfdM,2545
-dendrotweaks/morphology/point_trees.py,sha256=5dUPaQXYPdJbWoD3pFI2DV2XnuFRhB5d0wTBlfmmIeI,21600
+dendrotweaks/morphology/point_trees.py,sha256=aZl5p6FGn6mph9xNo-3L_HC7mIvLhvi3BLJuhuihssk,21605
 dendrotweaks/morphology/sec_trees.py,sha256=eKLC-yNhsn_rPdTE7w7p6STa1onYkBTGcpBKBpEWZUI,36957
 dendrotweaks/morphology/seg_trees.py,sha256=-XeSJuD7ZixBJYQDzvmSEiNvOWbVmX_DanyAPkkR-NA,4042
 dendrotweaks/morphology/trees.py,sha256=NrNvPMR-U0clt63eqwVJqU0H8NJgY53QGA_BkdcwkQI,16033
 dendrotweaks/morphology/io/__init__.py,sha256=gAZqZdf5VKPb6ksK8Lwt7MbTAq8TDP8uq3Vs_ebNFEY,324
-dendrotweaks/morphology/io/factories.py,sha256=DCE37QCloiYVro5HGihJbxPz91BB3y5NNf-oRaQ-M2g,6383
-dendrotweaks/morphology/io/reader.py,sha256=hW3c541WtG1rNag_YreEhvrLzm8-OTtw0fQREeHDthM,1913
+dendrotweaks/morphology/io/factories.py,sha256=YkTCXWuJ6bwUW0kjcV2TSzu43EvkE8N5yC3q-B02kxc,6372
+dendrotweaks/morphology/io/reader.py,sha256=ApfDdA-L61HLIqGbjOwiIntzO4P0_x3n4wYt8lsQzyU,2127
 dendrotweaks/morphology/io/validation.py,sha256=lVkYw9y9yG5QpRh_N0YQ3FbZwuSUsQfSqJTMumMcDdc,7872
 dendrotweaks/morphology/reduce/__init__.py,sha256=p6Mg3KDHxTt8S4DtI0m7L7MqV6dS2pdIYAwB7B-toVw,921
 dendrotweaks/morphology/reduce/reduce.py,sha256=5czZDrG3xsvHn3c_tbYhUOlXgST989-RS-ntbhlvvA0,6361
@@ -49,8 +52,8 @@ dendrotweaks/stimuli/__init__.py,sha256=bFfSEZhCVpwOVEBgLe65iiY3SdpjKPhyLemC1z5O
 dendrotweaks/stimuli/iclamps.py,sha256=NjkhhwZKJR1f_g3N9BVxMVoO9ubBk5WkQ6h9Bnf9xgA,1681
 dendrotweaks/stimuli/populations.py,sha256=vq2NUOaxaltUwlcT7wuCe8z1JWc8rk6HfPmfEd1kK68,8335
 dendrotweaks/stimuli/synapses.py,sha256=g4MgWTske2TZ2i9FIIOE8-KXNx_3dWa3zEhB2rcqYig,5470
-dendrotweaks-0.4.4.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-dendrotweaks-0.4.4.dist-info/METADATA,sha256=2eqzr1zuEY9kyPT0X0ggJ5m_lAqV2_sQKEtSX9TA9PQ,2740
-dendrotweaks-0.4.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-dendrotweaks-0.4.4.dist-info/top_level.txt,sha256=OzT_2BSI5j5zxC447K6Y-0W-GHbued7iX-_hFGAKMxY,13
-dendrotweaks-0.4.4.dist-info/RECORD,,
+dendrotweaks-0.4.6.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+dendrotweaks-0.4.6.dist-info/METADATA,sha256=OXESFIO9zc6MW9dmNJLg4dY-DrPqF6haGWPf8ut2kSg,2740
+dendrotweaks-0.4.6.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+dendrotweaks-0.4.6.dist-info/top_level.txt,sha256=OzT_2BSI5j5zxC447K6Y-0W-GHbued7iX-_hFGAKMxY,13
+dendrotweaks-0.4.6.dist-info/RECORD,,