pynamicalsys 1.2.2__py3-none-any.whl → 1.3.0__py3-none-any.whl

pynamicalsys/discrete_time/transport.py

@@ -44,7 +44,7 @@ def diffusion_coefficient(
     parameters : NDArray[np.float64]
         System parameters passed to mapping function
     total_time : int
-        Total evolution time (must be > transient_time)
+        Total evolution time
     mapping : Callable[[NDArray, NDArray], NDArray]
         System evolution function: u_next = mapping(u, parameters)
     axis : int, optional
@@ -58,7 +58,6 @@ def diffusion_coefficient(
     Raises
     ------
     ValueError
-        If total_time ≤ transient_time
         If axis index is invalid
 
     Notes
@@ -93,14 +92,12 @@ def average_vs_time(
     mapping: Callable[[NDArray[np.float64], NDArray[np.float64]], NDArray[np.float64]],
     sample_times: Optional[NDArray[np.int32]] = None,
     axis: int = 1,
-    transient_time: int = 0,
 ) -> NDArray[np.float64]:
     """
     Compute the time evolution of ensemble averages for a dynamical system.
 
     Tracks the average value of a specified coordinate across multiple trajectories,
-    with options for downsampling and transient removal. Useful for studying
-    convergence to equilibrium or statistical properties.
+    with options for downsampling. Useful for studying convergence to equilibrium or statistical properties.
 
     Parameters
     ----------
@@ -109,15 +106,13 @@ def average_vs_time(
     parameters : NDArray[np.float64]
         System parameters passed to mapping function
     total_time : int
-        Total number of iterations (must be > transient_time)
+        Total number of iterations
     mapping : Callable[[NDArray, NDArray], NDArray]
         System evolution function: u_next = mapping(u, parameters)
     sample_times : Optional[NDArray[np.int64]], optional
         Specific time steps to record (default: record all steps)
     axis : int, optional
         Coordinate index to analyze (default: 1)
-    transient_time : int, optional
-        Initial iterations to discard (default: 0)
 
     Returns
     -------
@@ -127,7 +122,6 @@ def average_vs_time(
     Raises
     ------
     ValueError
-        If total_time ≤ transient_time
         If sample_times contains values > total_time
         If axis is invalid
 
@@ -135,11 +129,9 @@ def average_vs_time(
     -----
     - Uses parallel processing over initial conditions
     - For large ensembles, consider using sample_times to reduce memory
-    - The output length matches len(sample_times) if provided, else (total_time - transient_time)
+    - The output length matches len(sample_times) if provided, else total_time
     """
     # Input validation
-    if total_time <= transient_time:
-        raise ValueError("total_time must be > transient_time")
     if axis < 0 or axis >= u.shape[1]:
         raise ValueError(f"axis must be in [0, {u.shape[1]-1}]")
     if sample_times is not None:
@@ -148,30 +140,26 @@ def average_vs_time(
 
     # Initialize tracking
     num_ic = u.shape[0]
-    effective_time = total_time - transient_time
     u_current = u.copy()
 
-    # Handle output array
+    # Handle output array and sample times
     if sample_times is not None:
         output = np.empty(len(sample_times))
     else:
-        output = np.empty(effective_time)
+        sample_times = np.arange(total_time) + 1
+        output = np.empty(total_time)
 
-    output_idx = 0
+    sample_idx = 0
 
-    # Main evolution loop
-    for t in range(total_time):
-        # Parallel evolution
-        for i in prange(num_ic):
-            u_current[i] = mapping(u_current[i], parameters)
-
-        # Record if past transient and matches sampling
-        if t >= transient_time:
-            output[output_idx] = np.mean(u_current[:, axis])
-            if sample_times is None:
-                output_idx += 1
-            elif t in sample_times:
-                output_idx += 1
+    prev_t = 0
+    for st in sample_times:
+        steps = st - prev_t
+        for _ in range(steps):
+            for i in prange(num_ic):
+                u_current[i] = mapping(u_current[i], parameters)
+        output[sample_idx] = np.mean(u_current[:, axis])
+        sample_idx += 1
+        prev_t = st
 
     return output
 
@@ -184,7 +172,6 @@ def cumulative_average_vs_time(
     mapping: Callable[[NDArray[np.float64], NDArray[np.float64]], NDArray[np.float64]],
     sample_times: Optional[NDArray[np.int32]] = None,
     axis: int = 1,
-    transient_time: int = 0,
 ) -> NDArray[np.float64]:
     """
     Compute the time evolution of the cumulative average of a coordinate across trajectories.
@@ -196,15 +183,13 @@ def cumulative_average_vs_time(
     parameters : NDArray[np.float64]
         System parameters passed to mapping function
     total_time : int
-        Total number of iterations (must be > transient_time)
+        Total number of iterations
     mapping : Callable[[NDArray, NDArray], NDArray]
         System evolution function: u_next = mapping(u, parameters)
     sample_times : Optional[NDArray[np.int64]], optional
         Specific time steps to record (default: record all steps)
     axis : int, optional
         Coordinate index to analyze (default: 1)
-    transient_time : int, optional
-        Initial iterations to discard (default: 0)
 
     Returns
     -------
@@ -214,7 +199,6 @@ def cumulative_average_vs_time(
     Raises
     ------
     ValueError
-        If total_time ≤ transient_time
         If sample_times contains invalid values
         If axis is invalid
 
@@ -222,39 +206,33 @@ def cumulative_average_vs_time(
     -----
     - Uses parallel processing over initial conditions
     - For large total_time, use sample_times to reduce memory usage
-    - The cumulative average is computed over the ensemble after removing transient
+    - The output length matches len(sample_times) if provided, else total_time
     """
 
     num_ic = u.shape[0]
     u_current = u.copy()
     sum_values = np.zeros(num_ic)
+    sample_idx = 0
 
-    # Initialize output array
+    # Handle output array and sample times
     if sample_times is not None:
-        output_size = len(sample_times)
+        output = np.empty(len(sample_times))
     else:
-        output_size = total_time - transient_time
-
-    cumul_average = np.zeros(output_size)
-    output_idx = 0
-
-    # Main evolution loop
-    for t in range(1, total_time + 1):
-        # Parallel evolution
-        for i in prange(num_ic):
-            u_current[i] = mapping(u_current[i], parameters)
-
-        # Record if past transient and matches sampling
-        if t > transient_time:
-            # Update running sum of squares
+        sample_times = np.arange(total_time, dtype=np.int64) + 1
+        output = np.empty(total_time)
+
+    prev_t = 0
+    for st in sample_times:
+        steps = st - prev_t
+        for _ in range(steps):
+            for i in prange(num_ic):
+                u_current[i] = mapping(u_current[i], parameters)
             sum_values += u_current[:, axis]
-            cumul_average[output_idx] = np.mean(sum_values / t)
-            if sample_times is None:
-                output_idx += 1
-            elif t in sample_times:
-                output_idx += 1
+        output[sample_idx] = np.mean(sum_values / st)
+        sample_idx += 1
+        prev_t = st
 
-    return cumul_average
+    return output
 
 
 @njit(cache=True, parallel=True)
@@ -265,7 +243,6 @@ def root_mean_squared(
     mapping: Callable[[NDArray[np.float64], NDArray[np.float64]], NDArray[np.float64]],
     sample_times: Optional[NDArray[np.int32]] = None,
     axis: int = 1,
-    transient_time: int = 0,
 ) -> NDArray[np.float64]:
     """
     Compute the time evolution of the root mean square (RMS) of a coordinate across trajectories.
@@ -281,15 +258,13 @@ def root_mean_squared(
     parameters : NDArray[np.float64]
         System parameters passed to mapping function
     total_time : int
-        Total number of iterations (must be > transient_time)
+        Total number of iterations
     mapping : Callable[[NDArray, NDArray], NDArray]
         System evolution function: u_next = mapping(u, parameters)
     sample_times : Optional[NDArray[np.int64]], optional
         Specific time steps to record (default: record all steps)
     axis : int, optional
         Coordinate index to analyze (default: 1)
-    transient_time : int, optional
-        Initial iterations to discard (default: 0)
 
     Returns
     -------
@@ -299,7 +274,6 @@ def root_mean_squared(
     Raises
     ------
     ValueError
-        If total_time ≤ transient_time
         If sample_times contains invalid values
         If axis is invalid
 
@@ -307,39 +281,34 @@ def root_mean_squared(
     -----
     - Uses parallel processing over initial conditions
     - For large total_time, use sample_times to reduce memory usage
-    - The RMS is computed over the ensemble after removing transient
+    - The output length matches len(sample_times) if provided, else total_time
     """
 
     num_ic = u.shape[0]
     u_current = u.copy()
     sum_squares = np.zeros(num_ic)
 
-    # Initialize output array
+    # Handle output array and sample times
     if sample_times is not None:
-        output_size = len(sample_times)
+        output = np.empty(len(sample_times))
     else:
-        output_size = total_time - transient_time
+        sample_times = np.arange(total_time) + 1
+        output = np.empty(total_time)
 
-    rms = np.zeros(output_size)
-    output_idx = 0
+    sample_idx = 0
 
-    # Main evolution loop
-    for t in range(1, total_time + 1):
-        # Parallel evolution
-        for i in prange(num_ic):
-            u_current[i] = mapping(u_current[i], parameters)
-
-        # Record if past transient and matches sampling
-        if t > transient_time:
-            # Update running sum of squares
+    prev_t = 0
+    for st in sample_times:  # st = sample time
+        steps = st - prev_t
+        for _ in range(steps):
+            for i in prange(num_ic):
+                u_current[i] = mapping(u_current[i], parameters)
             sum_squares += u_current[:, axis] ** 2
-            rms[output_idx] = np.sqrt(np.mean(sum_squares / t))
-            if sample_times is None:
-                output_idx += 1
-            elif t in sample_times:
-                output_idx += 1
+        output[sample_idx] = np.sqrt(np.mean(sum_squares / st))
+        sample_idx += 1
+        prev_t = st
 
-    return rms
+    return output
 
 
 @njit(cache=True, parallel=True)
@@ -350,7 +319,6 @@ def mean_squared_displacement(
     mapping: Callable[[NDArray[np.float64], NDArray[np.float64]], NDArray[np.float64]],
     sample_times: Optional[NDArray[np.int32]] = None,
     axis: int = 1,
-    transient_time: int = 0,
 ) -> NDArray[np.float64]:
     """
     Compute the mean squared displacement (MSD) of a coordinate across multiple trajectories.
@@ -366,15 +334,13 @@ def mean_squared_displacement(
     parameters : NDArray[np.float64]
         System parameters passed to mapping function
     total_time : int
-        Total number of iterations (must be > transient_time)
+        Total number of iterations
     mapping : Callable[[NDArray, NDArray], NDArray]
         System evolution function: u_next = mapping(u, parameters)
     sample_times : Optional[NDArray[np.int64]], optional
         Specific time steps to record (default: record all steps)
     axis : int, optional
         Coordinate index to analyze (default: 1)
-    transient_time : int, optional
-        Initial iterations to discard (default: 0)
 
     Returns
     -------
@@ -384,7 +350,6 @@ def mean_squared_displacement(
     Raises
     ------
     ValueError
-        If total_time ≤ transient_time
         If sample_times contains invalid values
         If axis is invalid
 
@@ -392,7 +357,8 @@ def mean_squared_displacement(
     -----
     - Uses parallel processing over initial conditions
     - For normal diffusion, MSD grows linearly with time
-    - The output length matches len(sample_times) if provided, else (total_time - transient_time)
+    - The output length matches len(sample_times) if provided, else total_time
+    - For large total_time, use sample_times to reduce memory usage
     """
     # Input validation
 
@@ -401,31 +367,27 @@ def mean_squared_displacement(
     # Store initial values for MSD calculation
     initial_values = u0[:, axis].copy()
 
-    # Initialize output array
+    # Handle output array and sample times
     if sample_times is not None:
-        output_size = len(sample_times)
+        output = np.empty(len(sample_times))
     else:
-        output_size = total_time - transient_time
-
-    msd = np.zeros(output_size)
-    output_idx = 0
-
-    # Main evolution loop
-    for t in range(1, total_time + 1):
-        # Parallel evolution
-        for i in prange(num_ic):
-            u[i] = mapping(u[i], parameters)
-
-        # Calculate and store MSD if past transient
-        if t > transient_time:
-            displacements = u[:, axis] - initial_values
-            msd[output_idx] = np.mean(displacements**2)
-            if sample_times is None:
-                output_idx += 1
-            elif t in sample_times:
-                output_idx += 1
-
-    return msd
+        sample_times = np.arange(total_time) + 1
+        output = np.empty(total_time)
+
+    sample_idx = 0
+
+    prev_t = 0
+    for st in sample_times:
+        steps = st - prev_t
+        for _ in range(steps):
+            for i in prange(num_ic):
+                u[i] = mapping(u[i], parameters)
+        displacements = u[:, axis] - initial_values
+        output[sample_idx] = np.mean(displacements**2)
+        sample_idx += 1
+        prev_t = st
+
+    return output
 
 
 @njit(cache=True)

pynamicalsys/discrete_time/validators.py

@@ -278,7 +278,7 @@ def validate_sample_times(sample_times, total_time):
         return None
 
     try:
-        sample_times_arr = np.asarray(sample_times, dtype=np.int32)
+        sample_times_arr = np.asarray(sample_times, dtype=np.int64)
         if sample_times_arr.ndim != 1:
             raise ValueError("sample_times must be a 1D array")
         if np.any(sample_times_arr < 0) or np.any(sample_times_arr > total_time):

{pynamicalsys-1.2.2.dist-info → pynamicalsys-1.3.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pynamicalsys
-Version: 1.2.2
+Version: 1.3.0
 Summary: A Python toolkit for the analysis of dynamical systems
 Author-email: Matheus Rolim Sales <rolim.sales.m@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -733,7 +733,7 @@ $ pip install pynamicalsys
 To upgrade your current version of **pynamicalsys** to the latest stable release, run in your command line:
 
 ```bash
-$ pip install **pynamicalsys** --upgrade
+$ pip install pynamicalsys --upgrade
 ```
 
 ### Install from source
@@ -781,7 +781,7 @@ Currently, our research paper is under review, but in the mean time, if you use
 
 ## Contributing
 
-We welcome contributions from the community! To get started, please see our Contributing Guidelines.
+We welcome contributions from the community! To get started, please see our [Contributing Guidelines](https://pynamicalsys.readthedocs.io/en/latest/contributing.html).
 
 ## License
 

{pynamicalsys-1.2.2.dist-info → pynamicalsys-1.3.0.dist-info}/RECORD

@@ -1,28 +1,28 @@
 pynamicalsys/__init__.py,sha256=IBHDcCD7wX8pULFXLk0yvF3uuNodvDKGirJektm1nR4,1215
-pynamicalsys/__version__.py,sha256=o0zEAUXpMoJZCULVYplCdjcZuIQ-3sIIZKyfNu_loQE,511
+pynamicalsys/__version__.py,sha256=0Oc4EBzGTJOvXX0Vym4evglW1NQPpe8RLn8TdxsKzfs,704
 pynamicalsys/common/__init__.py,sha256=W4OESm7TA-EUTGUOtIgBgvSd1n80Mgl0KA2dCkw8yIw,721
 pynamicalsys/common/basin_analysis.py,sha256=teGEOMPPOdzKNZsN0_OvkzBlcV-UOANRjcdFyI2-FLM,5473
 pynamicalsys/common/recurrence_quantification_analysis.py,sha256=neBolgoWrGJYOQta71Jf2ZMwNK1RoaZb_wNHqb1mM7I,14356
-pynamicalsys/common/utils.py,sha256=ezNMSGTDVjtHpAa95Dr0r09s5CR_h9AShLU_ZuLMM44,10189
+pynamicalsys/common/utils.py,sha256=-sPpnoC3G8fJmdGZHzyQvbYU3Ym3BUMBlklaTgcz_Ac,10304
 pynamicalsys/continuous_time/__init__.py,sha256=W4OESm7TA-EUTGUOtIgBgvSd1n80Mgl0KA2dCkw8yIw,721
-pynamicalsys/continuous_time/chaotic_indicators.py,sha256=rwstGDMx2ynT7woezVqaOQ10HJpblp0dJvheLjpCnBg,9891
+pynamicalsys/continuous_time/chaotic_indicators.py,sha256=UNZL1yJvUAvFC-RD-Xr3xZIEFCXgdpgw8KzmTh7U9OU,12542
 pynamicalsys/continuous_time/models.py,sha256=YJtmsVZqSn3GDNqV0IKSQBHWZSCDY_EJ5Sgh4ulDc9I,5339
-pynamicalsys/continuous_time/numerical_integrators.py,sha256=pSsDIlxhSntLxfHLRNduqjExdiUEY6yNpQRyvLBraqk,9667
-pynamicalsys/continuous_time/trajectory_analysis.py,sha256=1Eh4WEIlLT_fFGfgEorSgN1qGZ9ym0kVEPbWcRRXNKQ,4406
+pynamicalsys/continuous_time/numerical_integrators.py,sha256=CtP8GWNWGE5_2FYnrpbKFZMKklJdZBDWq3FkeXoIG2U,9684
+pynamicalsys/continuous_time/trajectory_analysis.py,sha256=hpoEw0EZLRV3UoWEGM7P7rH6LLY8lRNZXJ2ymQnNNDw,5256
 pynamicalsys/continuous_time/validators.py,sha256=dvtlcWbn2w5_vNUB68f7ywFPyFrPKe3cUDqGCk52mhw,3834
 pynamicalsys/core/__init__.py,sha256=W4OESm7TA-EUTGUOtIgBgvSd1n80Mgl0KA2dCkw8yIw,721
 pynamicalsys/core/basin_metrics.py,sha256=sqSj-UCzBQdRaTvOBtzo8SCgJN90T3GiWy4nlLsbg5c,7604
-pynamicalsys/core/continuous_dynamical_systems.py,sha256=nkESGfuxBT_UmoY_2tJv1fMY4hK1J0M74aQpLgNVEyI,30482
-pynamicalsys/core/discrete_dynamical_systems.py,sha256=AhxyAOZFnkjf4KnJiaReN5ZRndkFFEG_GOT2_PeLpXs,135874
+pynamicalsys/core/continuous_dynamical_systems.py,sha256=uunVcArRk5JEG0Z1G8KqlmYDxVzPokoeqNSXzXvUZN8,37989
+pynamicalsys/core/discrete_dynamical_systems.py,sha256=JcDL71M3kaQJLnkWOVTG28ylolNmitMg1tlpq3EryQA,145975
 pynamicalsys/core/plot_styler.py,sha256=sVX_rb1HSt340U3zyPlXojylhma9cKCOgYirMIge18M,5647
 pynamicalsys/core/time_series_metrics.py,sha256=7fwXO1I6lIjmv_MzYxBn-9k2gjjnhm_y_Tp3diE1z68,5102
 pynamicalsys/discrete_time/__init__.py,sha256=W4OESm7TA-EUTGUOtIgBgvSd1n80Mgl0KA2dCkw8yIw,721
-pynamicalsys/discrete_time/dynamical_indicators.py,sha256=Ck6orYxy09NHsVYnTSmkROq33csiyiePdsqzOAJCKcs,43057
+pynamicalsys/discrete_time/dynamical_indicators.py,sha256=XDZ6e-nFCDO7UgkkBnuqsr70c3LLJ8bvew82pXrV1no,51759
 pynamicalsys/discrete_time/models.py,sha256=u9MlaCzBzR_OomWRYbEC2sS2qpfDg7qzZjX8YDijVe0,10756
 pynamicalsys/discrete_time/trajectory_analysis.py,sha256=W3nqLJgqJYMV9DbBbSSOpzNDQ7XlroP3lC0sgSoFztY,48669
-pynamicalsys/discrete_time/transport.py,sha256=29leQue2ReRbFzT_riqWXTZDvf2O7jMsMOUnAQPBrBU,15972
-pynamicalsys/discrete_time/validators.py,sha256=4eWQAlZgCzFsrmijzVF10CZuoIMiu-jvrrvRokBFTkY,10013
-pynamicalsys-1.2.2.dist-info/METADATA,sha256=UQDElv3HVAqJDDUM0251dJVDbQZPhyLTMe-hnHfPK-E,45834
-pynamicalsys-1.2.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-pynamicalsys-1.2.2.dist-info/top_level.txt,sha256=1AqoHXye_hGRkvqu4KY0SdEuNTgqf3xyTlV8xhiJJFU,13
-pynamicalsys-1.2.2.dist-info/RECORD,,
+pynamicalsys/discrete_time/transport.py,sha256=mp6jqI8zfqwVrV5ZXqyOaFKzAjuCPXl6pQtzmX-gDok,14429
+pynamicalsys/discrete_time/validators.py,sha256=sk5PuQ6vxNj6ReqIfBTb2iQqlgY0SUkndS56xcp3w_w,10013
+pynamicalsys-1.3.0.dist-info/METADATA,sha256=_A4OpfJ39pd-eGH-HY08lyuq-KcDbDZB6ktdNb-uWwk,45897
+pynamicalsys-1.3.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+pynamicalsys-1.3.0.dist-info/top_level.txt,sha256=1AqoHXye_hGRkvqu4KY0SdEuNTgqf3xyTlV8xhiJJFU,13
+pynamicalsys-1.3.0.dist-info/RECORD,,