osiris-utils 1.1.2__py3-none-any.whl → 1.1.4__py3-none-any.whl

osiris_utils/postprocessing/fft.py

@@ -0,0 +1,240 @@
+from ..utils import *
+from ..data.simulation import Simulation
+from .postprocess import PostProcess
+from ..data.diagnostic import Diagnostic
+import numpy as np
+import tqdm as tqdm
+
+
+class FastFourierTransform_Simulation(PostProcess):
+    """
+    Class to handle the Fast Fourier Transform on data. Works as a wrapper for the FFT_Diagnostic class.
+    Inherits from PostProcess to ensure all operation overloads work properly.
+    
+    Parameters
+    ----------
+    
+    simulation : Simulation
+        The simulation object.
+    axis : int
+        The axis to compute the FFT.
+
+    Example
+    -------
+    >>> sim = Simulation('electrons', 'path/to/simulation')
+    >>> fft = FastFourierTransform(sim, 1)
+    >>> fft_e1 = fft['e1']
+    """
+    def __init__(self, simulation, fft_axis):
+        super().__init__("FFT")
+        if not isinstance(simulation, Simulation):
+            raise ValueError("Simulation must be a Simulation object.")
+        self._simulation = simulation
+        self._fft_axis = fft_axis
+        self._fft_computed = {}
+        self._species_handler = {}
+
+    def __getitem__(self, key):
+        if key in self._simulation._species:
+            if key not in self._species_handler:
+                self._species_handler[key] = FFT_Species_Handler(self._simulation[key], self._fft_axis)
+            return self._species_handler[key]
+        
+        if key not in self._fft_computed:
+            self._fft_computed[key] = FFT_Diagnostic(self._simulation[key], self._fft_axis)
+        return self._fft_computed[key]
+    
+    def delete_all(self):
+        self._fft_computed = {}
+
+    def delete(self, key):
+        if key in self._fft_computed:
+            del self._fft_computed[key]
+        else:
+            print(f"FFT {key} not found in simulation")
+
+    def process(self, diagnostic):
+        """Apply FFT to a diagnostic"""
+        return FFT_Diagnostic(diagnostic, self._fft_axis)
+    
+
+class FFT_Diagnostic(Diagnostic):
+    """
+    Auxiliar class to compute the FFT of a diagnostic, for it to be similar in behavior to a Diagnostic object.
+    Inherits directly from Diagnostic to ensure all operation overloads work properly.
+
+    Parameters
+    ---------- 
+    diagnostic : Diagnostic
+        The diagnostic to compute the FFT.
+    axis : int
+        The axis to compute the FFT.
+
+    Methods
+    -------
+    load_all()
+        Load all the data and compute the FFT.
+    omega()
+        Get the angular frequency array for the FFT.
+    __getitem__(index)
+        Get data at a specific index.
+    
+    Example
+    -------
+    >>> sim = Simulation('electrons', 'path/to/simulation')
+    >>> diag = sim['e1']
+    >>> fft = FFT_Diagnostic(diag, 1)
+    """
+    def __init__(self, diagnostic, fft_axis):
+        if hasattr(diagnostic, '_species'):
+            super().__init__(simulation_folder=diagnostic._simulation_folder if hasattr(diagnostic, '_simulation_folder') else None, 
+                             species=diagnostic._species)
+        else:
+            super().__init__(None)
+
+        self._name = f"FFT[{diagnostic._name}, {fft_axis}]"
+        self._diag = diagnostic
+        self._fft_axis = fft_axis
+        self._data = None
+        self._all_loaded = False
+        
+        # Copy all relevant attributes from diagnostic
+        for attr in ['_dt', '_dx', '_ndump', '_axis', '_nx', '_x', '_grid', '_dim', '_maxiter']:
+            if hasattr(diagnostic, attr):
+                setattr(self, attr, getattr(diagnostic, attr))
+
+        if isinstance(self._dx, (int, float)):
+            self._kmax = np.pi / (self._dx) 
+        else:
+            self._kmax = np.pi / np.array([self._dx[ax-1] for ax in self._fft_axis if ax != 0])
+    
+    def load_all(self):
+        if self._data is not None:
+            print("Using cached derivative")
+            return self._data
+        
+        if not hasattr(self._diag, '_data') or self._diag._data is None:
+            self._diag.load_all()
+            self._diag._data = np.nan_to_num(self._diag._data)
+
+       # Apply appropriate windows based on which axes we're transforming
+        if isinstance(self._fft_axis, (list, tuple)):
+            # Multiple axes FFT
+            result = self._diag._data.copy()
+            
+            for axis in self._fft_axis:
+                if axis == 0:  # Time axis
+                    window = np.hanning(result.shape[0]).reshape(-1, *([1] * (result.ndim - 1)))
+                    result = result * window
+                else:  # Spatial axis
+                    window = self._get_window(result.shape[axis], axis)
+                    result = self._apply_window(result, window, axis)
+                    
+            with tqdm.tqdm(total=1, desc="FFT calculation") as pbar:
+                data_fft = np.fft.fftn(result, axes=self._fft_axis)
+                pbar.update(0.5)
+                result = np.fft.fftshift(data_fft, axes=self._fft_axis)
+                pbar.update(0.5)
+        
+        else:
+            if self._fft_axis == 0:
+                hanning_window = np.hanning(self._diag._data.shape[0]).reshape(-1, *([1] * (self._diag._data.ndim - 1)))
+                data_windowed = hanning_window * self._diag._data
+            else: 
+                window = self._get_window(self._diag._data.shape[self._fft_axis], self._fft_axis)
+                data_windowed = self._apply_window(self._diag._data, window, self._fft_axis)
+            
+            with tqdm.tqdm(total=1, desc="FFT calculation") as pbar:
+                data_fft = np.fft.fft(data_windowed, axis=self._fft_axis)
+                pbar.update(0.5)
+                result = np.fft.fftshift(data_fft, axes=self._fft_axis)
+                pbar.update(0.5)
+
+        self.omega_max = np.pi / self._dt / self._ndump
+
+        self._all_loaded = True
+        self._data = np.abs(result)**2
+        return self._data
+    
+    def _data_generator(self, index):
+        # Get the data for this index
+        original_data = self._diag[index]
+        
+        if self._fft_axis == 0:
+            raise ValueError("Cannot generate FFT along time axis for a single timestep. Use load_all() instead.")
+        
+        # For spatial FFT, we can apply a spatial window if desired
+        if isinstance(self._fft_axis, (list, tuple)):
+            result = original_data
+            for axis in self._fft_axis:
+                if axis != 0:  # Skip time axis
+                    # Apply window along this spatial dimension
+                    window = self._get_window(original_data.shape[axis-1], axis-1)
+                    result = self._apply_window(result, window, axis-1)
+                    
+            # Compute FFT
+            result_fft = np.fft.fftn(result, axes=[ax-1 for ax in self._fft_axis if ax != 0])
+            result_fft = np.fft.fftshift(result_fft, axes=[ax-1 for ax in self._fft_axis if ax != 0])
+            
+        else:
+            if self._fft_axis > 0:  # Spatial axis
+                window = self._get_window(original_data.shape[self._fft_axis-1], self._fft_axis-1)
+                windowed_data = self._apply_window(original_data, window, self._fft_axis-1)
+                
+                result_fft = np.fft.fft(windowed_data, axis=self._fft_axis-1)
+                result_fft = np.fft.fftshift(result_fft, axes=self._fft_axis-1)
+        
+        yield np.abs(result_fft)**2
+        
+    def _get_window(self, length, axis):
+        return np.hanning(length)
+
+    def _apply_window(self, data, window, axis):
+        ndim = data.ndim
+        window_shape = [1] * ndim
+        window_shape[axis] = len(window)
+        
+        reshaped_window = window.reshape(window_shape)
+        
+        return data * reshaped_window
+
+    def __getitem__(self, index):
+        if self._all_loaded and self._data is not None:
+            return self._data[index]
+        
+        if isinstance(index, int):
+            return next(self._data_generator(index))
+        elif isinstance(index, slice):
+            start = 0 if index.start is None else index.start
+            step = 1 if index.step is None else index.step
+            stop = self._diag._maxiter if index.stop is None else index.stop
+            return np.array([next(self._data_generator(i)) for i in range(start, stop, step)])
+        else:
+            raise ValueError("Invalid index type. Use int or slice.")
+    
+    def omega(self):
+        """
+        Get the angular frequency array for the FFT.
+        """
+        if not self._all_loaded:
+            raise ValueError("Load the data first using load_all() method.")
+        
+        omega = np.fft.fftfreq(self._data.shape[self._fft_axis], d=self._dx[self._fft_axis-1])
+        omega = np.fft.fftshift(omega)
+        return omega
+    
+    @property
+    def kmax(self):
+        return self._kmax
+    
+class FFT_Species_Handler:
+    def __init__(self, species_handler, fft_axis):
+        self._species_handler = species_handler
+        self._fft_axis = fft_axis
+        self._fft_computed = {}
+
+    def __getitem__(self, key):
+        if key not in self._fft_computed:
+            diag = self._species_handler[key]
+            self._fft_computed[key] = FFT_Diagnostic(diag, self._fft_axis)
+        return self._fft_computed[key]

osiris_utils/postprocessing/mft.py

@@ -0,0 +1,348 @@
+from ..utils import *
+from ..data.simulation import Simulation
+from .postprocess import PostProcess
+from ..data.diagnostic import Diagnostic
+
+class MeanFieldTheory_Simulation(PostProcess):
+    """
+    Class to compute the mean field theory of a diagnostic. Works as a wrapper for the MFT_Diagnostic class.
+    Inherits from PostProcess to ensure all operation overloads work properly.
+
+    Parameters
+    ----------
+    simulation : Simulation
+        The simulation object.
+    mft_axis : int
+        The axis to compute the mean field theory.
+
+    Example
+    -------
+    >>> sim = Simulation('electrons', 'path/to/simulation')
+    >>> mft = MeanFieldTheory(sim, 1)
+    >>> mft_e1 = mft['e1']
+    """
+
+    def __init__(self, simulation, mft_axis=None):
+        super().__init__(f"MeanFieldTheory({mft_axis})")
+        if not isinstance(simulation, Simulation):
+            raise ValueError("Simulation must be a Simulation object.")
+        self._simulation = simulation
+        self._mft_axis = mft_axis
+        self._mft_computed = {}
+        self._species_handler = {}
+
+    def __getitem__(self, key):
+        if key in self._simulation._species:
+            if key not in self._species_handler:
+                self._species_handler[key] = MFT_Species_Handler(self._simulation[key], self._mft_axis)
+            return self._species_handler[key]
+        if key not in self._mft_computed:
+            self._mft_computed[key] = MFT_Diagnostic(self._simulation[key], self._mft_axis)
+        return self._mft_computed[key]
+    
+    def delete_all(self):
+        self._mft_computed = {}
+
+    def delete(self, key):
+        if key in self._mft_computed:
+            del self._mft_computed[key]
+        else:
+            print(f"MeanFieldTheory {key} not found in simulation")
+
+    def process(self, diagnostic):
+        """Apply mean field theory to a diagnostic"""
+        return MFT_Diagnostic(diagnostic, self._mft_axis)
+
+class MFT_Diagnostic(Diagnostic):
+    """
+    Class to compute mean field theory of a diagnostic.
+    Acts as a container for the average and fluctuation components.
+
+    Parameters
+    ----------
+    diagnostic : Diagnostic
+        The diagnostic object.
+    mft_axis : int
+        The axis to compute mean field theory along.
+
+    Example
+    -------
+    >>> sim = Simulation('electrons', 'path/to/simulation')
+    >>> diag = sim['e1']
+    >>> mft = MFT_Diagnostic(diag, 1)
+    >>> avg = mft['avg']
+    >>> delta = mft['delta']
+    """
+
+    def __init__(self, diagnostic, mft_axis):
+        # Initialize using parent's __init__ with the same species
+        if hasattr(diagnostic, '_species'):
+            super().__init__(species=diagnostic._species)
+        else:
+            super().__init__(None)
+            
+        self._name = f"MFT[{diagnostic._name}]"
+        self._diag = diagnostic
+        self._mft_axis = mft_axis
+        self._data = None
+        self._all_loaded = False
+        
+        # Components that will be lazily created
+        self._components = {}
+        
+        # Copy all relevant attributes from diagnostic
+        for attr in ['_dt', '_dx', '_ndump', '_axis', '_nx', '_x', '_grid', '_dim', '_maxiter']:
+            if hasattr(diagnostic, attr):
+                setattr(self, attr, getattr(diagnostic, attr))
+
+    def __getitem__(self, key):
+        """
+        Get a component of the mean field theory.
+        
+        Parameters
+        ----------
+        key : str
+            Either "avg" for average or "delta" for fluctuations.
+        
+        Returns
+        -------
+        Diagnostic
+            The requested component.
+        """
+        if key == "avg":
+            if "avg" not in self._components:
+                self._components["avg"] = MFT_Diagnostic_Average(self._diag, self._mft_axis)
+            return self._components["avg"]
+        
+        elif key == "delta":
+            if "delta" not in self._components:
+                self._components["delta"] = MFT_Diagnostic_Fluctuations(self._diag, self._mft_axis)
+            return self._components["delta"]
+        
+        else:
+            raise ValueError("Invalid MFT component. Use 'avg' or 'delta'.")
+    
+    def load_all(self):
+        """Load both average and fluctuation components"""
+        # This will compute both components at once for efficiency
+        if "avg" not in self._components:
+            self._components["avg"] = MFT_Diagnostic_Average(self._diag, self._mft_axis)
+        
+        if "delta" not in self._components:
+            self._components["delta"] = MFT_Diagnostic_Fluctuations(self._diag, self._mft_axis)
+        
+        # Load both components
+        self._components["avg"].load_all()
+        self._components["delta"].load_all()
+        
+        # Mark this container as loaded
+        self._all_loaded = True
+        
+        return self._components
+
+class MFT_Diagnostic_Average(Diagnostic):
+    """
+    Class to compute the average component of mean field theory.
+    Inherits from Diagnostic to ensure all operation overloads work properly.
+
+    Parameters
+    ----------
+    diagnostic : Diagnostic
+        The diagnostic object.
+    mft_axis : int
+        The axis to compute the mean field theory.
+
+    Example
+    -------
+    >>> sim = Simulation('electrons', 'path/to/simulation')
+    >>> diag = sim['e1']
+    >>> avg = MFT_Diagnostic_Average(diag, 1)
+    """
+
+    def __init__(self, diagnostic, mft_axis):
+        # Initialize with the same species as the diagnostic
+        if hasattr(diagnostic, '_species'):
+            super().__init__(species=diagnostic._species)
+        else:
+            super().__init__(None)
+            
+        if mft_axis is None:
+            raise ValueError("Mean field theory axis must be specified.")
+        
+        self._name = f"MFT_avg[{diagnostic._name}, {mft_axis}]"
+        self._diag = diagnostic
+        self._mft_axis = mft_axis
+        self._data = None
+        self._all_loaded = False
+
+        # Copy all relevant attributes from diagnostic
+        for attr in ['_dt', '_dx', '_ndump', '_axis', '_nx', '_x', '_grid', '_dim', '_maxiter']:
+            if hasattr(diagnostic, attr):
+                setattr(self, attr, getattr(diagnostic, attr))
+
+    def load_all(self):
+        """Load all data and compute the average"""
+        if self._data is not None:
+            print("Data already loaded")
+            return self._data
+        
+        if not hasattr(self._diag, '_data') or self._diag._data is None:
+            self._diag.load_all()
+
+        if self._mft_axis is None:
+            raise ValueError("Mean field theory axis must be specified.")
+        else:
+            self._data = np.expand_dims(self._diag._data.mean(axis=self._mft_axis), axis=-1)
+
+        self._all_loaded = True
+        return self._data
+    
+    def _data_generator(self, index):
+        """Generate average data for a specific index"""
+        if self._mft_axis is not None:
+            # Get the data for this index
+            data = self._diag[index]
+            # Compute the average (mean) along the specified axis
+            # Note: When accessing a slice, axis numbering is 0-based
+            avg = np.expand_dims(data.mean(axis=self._mft_axis-1), axis=-1)
+            yield avg
+        else:
+            raise ValueError("Invalid axis for mean field theory.")
+        
+    def __getitem__(self, index):
+        """Get average at a specific index"""
+        if self._all_loaded and self._data is not None:
+            return self._data[index]
+        
+        # Otherwise compute on-demand
+        if isinstance(index, int):
+            return next(self._data_generator(index))
+        elif isinstance(index, slice):
+            start = 0 if index.start is None else index.start
+            step = 1 if index.step is None else index.step
+            stop = self._diag._maxiter if index.stop is None else index.stop
+            return np.array([next(self._data_generator(i)) for i in range(start, stop, step)])
+        else:
+            raise ValueError("Invalid index type. Use int or slice.")
+    
+class MFT_Diagnostic_Fluctuations(Diagnostic):
+    """
+    Class to compute the fluctuation component of mean field theory.
+    Inherits from Diagnostic to ensure all operation overloads work properly.
+
+    Parameters
+    ----------
+    diagnostic : Diagnostic
+        The diagnostic object.
+    mft_axis : int
+        The axis to compute the mean field theory.
+
+    Example
+    -------
+    >>> sim = Simulation('electrons', 'path/to/simulation')
+    >>> diag = sim['e1']
+    >>> delta = MFT_Diagnostic_Fluctuations(diag, 1)
+    """
+    
+    def __init__(self, diagnostic, mft_axis):
+        # Initialize with the same species as the diagnostic
+        if hasattr(diagnostic, '_species'):
+            super().__init__(species=diagnostic._species)
+        else:
+            super().__init__(None)
+            
+        if mft_axis is None:
+            raise ValueError("Mean field theory axis must be specified.")
+        
+        self._name = f"MFT_delta[{diagnostic._name}, {mft_axis}]"
+        self._diag = diagnostic
+        self._mft_axis = mft_axis
+        self._data = None
+        self._all_loaded = False
+
+        # Copy all relevant attributes from diagnostic
+        for attr in ['_dt', '_dx', '_ndump', '_axis', '_nx', '_x', '_grid', '_dim', '_maxiter']:
+            if hasattr(diagnostic, attr):
+                setattr(self, attr, getattr(diagnostic, attr))
+
+    def load_all(self):
+        """Load all data and compute the fluctuations"""
+        if self._data is not None:
+            print("Data already loaded")
+            return self._data
+        
+        if not hasattr(self._diag, '_data') or self._diag._data is None:
+            self._diag.load_all()
+
+        if self._mft_axis is None:
+            raise ValueError("Mean field theory axis must be specified.")
+        else:
+            # Compute the average
+            avg = self._diag._data.mean(axis=self._mft_axis)
+            # Reshape avg for broadcasting
+            broadcast_shape = list(self._diag._data.shape)
+            broadcast_shape[self._mft_axis] = 1
+            avg_reshaped = avg.reshape(broadcast_shape)
+            # Compute the fluctuations
+            self._data = self._diag._data - avg_reshaped
+
+        self._all_loaded = True
+        return self._data
+    
+    def _data_generator(self, index):
+        """Generate fluctuation data for a specific index"""
+        if self._mft_axis is not None:
+            # Get the data for this index
+            data = self._diag[index]
+            # Compute the average (mean) along the specified axis
+            # Note: When accessing a slice, axis numbering is 0-based
+            avg = data.mean(axis=self._mft_axis-1)
+            # Expand dimensions to enable broadcasting
+            avg_reshaped = np.expand_dims(avg, axis=self._mft_axis-1)
+            # Compute fluctuations
+            delta = data - avg_reshaped
+            yield delta
+        else:
+            raise ValueError("Invalid axis for mean field theory.")
+        
+    def __getitem__(self, index):
+        """Get fluctuations at a specific index"""
+        if self._all_loaded and self._data is not None:
+            return self._data[index]
+        
+        # Otherwise compute on-demand
+        if isinstance(index, int):
+            return next(self._data_generator(index))
+        elif isinstance(index, slice):
+            start = 0 if index.start is None else index.start
+            step = 1 if index.step is None else index.step
+            stop = self._diag._maxiter if index.stop is None else index.stop
+            return np.array([next(self._data_generator(i)) for i in range(start, stop, step)])
+        else:
+            raise ValueError("Invalid index type. Use int or slice.")
+    
+class MFT_Species_Handler:
+    """
+    Class to handle mean field theory for a species.
+    Acts as a wrapper for the MFT_Diagnostic class.
+
+    Not intended to be used directly, but through the MFT_Simulation class.
+
+    Parameters
+    ----------
+    species_handler : Species_Handler
+        The species handler object.
+    mft_axis : int
+        The axis to compute the mean field theory.
+    """
+    
+    def __init__(self, species_handler, mft_axis):
+        self._species_handler = species_handler
+        self._mft_axis = mft_axis
+        self._mft_computed = {}
+
+    def __getitem__(self, key):
+        if key not in self._mft_computed:
+            diag = self._species_handler[key]
+            self._mft_computed[key] = MFT_Diagnostic(diag, self._mft_axis)
+        return self._mft_computed[key]

osiris_utils/postprocessing/mft_for_gridfile.py

@@ -0,0 +1,52 @@
+import numpy as np
+from ..data.data import OsirisGridFile
+
+# Deprecated
+class MFT_Single(OsirisGridFile):
+    '''
+    Class to handle the mean field theory on data. Inherits from OsirisGridFile.
+    
+    Parameters
+    ----------
+    source : str or OsirisGridFile
+        The filename or an OsirisGridFile object.
+    axis : int
+        The axis to average over.
+    '''
+    def __init__(self, source, axis=1):
+        if isinstance(source, OsirisGridFile):
+            self.__dict__.update(source.__dict__)
+        else:
+            super().__init__(source)
+        self._compute_mean_field(axis=axis)
+
+    def _compute_mean_field(self, axis=1):
+        self._average = np.expand_dims(np.mean(self.data, axis=axis), axis=axis)
+        self._fluctuations = self.data - self._average
+
+    def __array__(self):
+        return self.data
+
+    @property
+    def average(self):
+        return self._average
+    
+    @property
+    def delta(self):
+        return self._fluctuations
+    
+    def __str__(self):
+        return super().__str__() + f'\nAverage: {self.average.shape}\nDelta: {self.delta.shape}'
+    
+    def derivative(self, field, axis=0):
+        '''
+        Compute the derivative of the average or the fluctuations.
+        
+        Parameters
+        ----------
+        field : MeanFieldTheory.average or MeanFieldTheory.delta
+            The field to compute the derivative.
+        axis : int
+            The axis to compute the derivative.
+        '''
+        return np.gradient(field, self.dx[axis], axis=0)

osiris_utils/postprocessing/postprocess.py

@@ -0,0 +1,42 @@
+from ..data.diagnostic import Diagnostic
+
+class PostProcess(Diagnostic):
+    """
+    Base class for post-processing operations.
+    Inherits from Diagnostic to ensure all operation overloads work.
+    
+    Parameters
+    ----------
+    name : str
+        Name of the post-processing operation.
+    species : str
+        The species to analyze.
+    """
+    
+    def __init__(self, name, species=None):
+        # Initialize with the same interface as Diagnostic
+        super().__init__(species)
+        self._name = name
+        self._all_loaded = False
+        self._data = None
+        
+    def process(self, diagnostic):
+        """
+        Apply the post-processing to a diagnostic.
+        Must be implemented by subclasses.
+        
+        Parameters
+        ----------
+        diagnostic : Diagnostic
+            The diagnostic to process.
+            
+        Returns
+        -------
+        Diagnostic or PostProcess
+            The processed diagnostic.
+        """
+        raise NotImplementedError("Subclasses must implement process method")
+    
+
+# PostProcessing_Simulation
+# PostProcessing_Diagnostic