osiris-utils 1.1.3__py3-none-any.whl → 1.1.6__py3-none-any.whl

osiris_utils/utils.py

@@ -4,6 +4,7 @@ import matplotlib.pyplot as plt
 import matplotlib.animation as animation
 import scipy 
 import pandas as pd
+from datetime import datetime
 
 def courant2D(dx, dy):
     '''
@@ -24,7 +25,7 @@ def courant2D(dx, dy):
     dt = 1 / (np.sqrt(1/dx**2 + 1/dy**2))
     return dt
 
-def time_estimation(n_cells, ppc, push_time, t_steps, n_cpu, hours = False):
+def time_estimation(n_cells, ppc, t_steps, n_cpu, push_time = 1e-7, hours = False):
     '''
     Estimate the simulation time.
 
@@ -106,45 +107,6 @@ def integrate(array, dx):
     int = -scipy.integrate.cumulative_simpson(flip_array, dx = dx, initial = 0)
     return np.flip(int)
 
-def animate_2D(datafiles, frames, interval, fps, savename, **kwargs):
-    '''
-    Animate 2D OSIRIS files.
-
-    Parameters
-    ----------
-    datafiles : str
-        The path to the files.
-        Must be of the type 'path/to/file_%06d.h5'.
-    kwargs : dict
-        Additional keyword arguments for plotting.
-
-    Returns
-    -------
-    matplotlib.animation.FuncAnimation
-        The animation.
-    '''
-    fig, ax = plt.subplots(figsize=(12, 6), tight_layout=True)
-    im = 0
-
-    def animate(i):
-        # Assuming this returns (x, y, data, out) correctly
-        x, y, data, _ = open2D(datafiles % i)
-        ax.clear()
-        # Display image data, make sure data shape is valid for imshow
-        im = ax.imshow(-data, extent=[x.min(), x.max(), y.min(), y.max()], aspect='auto', origin='lower', **kwargs)
-        plt.xlabel(r'x [c/$\omega_p$]')
-        plt.ylabel(r'y [c/$\omega_p$]')
-        
-
-    # Creating the animation, and frames should be updated accordingly
-    ani = animation.FuncAnimation(fig, animate, frames=frames, interval=interval)
-
-    # Save the animation as a GIF (you can set the path and filename)
-    ani.save(savename, writer='pillow', fps=fps)  # fps can be adjusted
-
-    # Display the animation
-    return ani
-
 def save_data(data, savename, option='numpy'):
     """
     Save the data to a .txt (with Numpy) or .csv (with Pandas) file.
@@ -180,4 +142,142 @@ def read_data(filename, option='numpy'):
         Dim: 2D.
         The data.
     '''
-    return np.loadtxt(filename) if option == 'numpy' else pd.read_csv(filename).values
+    return np.loadtxt(filename) if option == 'numpy' else pd.read_csv(filename).values
+
+
+def convert_tracks(filename_in):
+    '''
+   Converts a new OSIRIS track file aka IDL-formatted aka tracks-2 to an older format that is more human-readable.  
+   In the old format, each particle is stored in a separate folder, with datasets for each quantity.  
+   The function reads data from the input file, processes it, and writes it to a new file with the suffix "-v2".
+
+    code from https://github.com/GoLP-IST/RaDi-x/blob/main/tools/convert_idl_tracks_py3.py 
+
+    Parameters
+    ----------
+    filename_in : str
+        The path to the trackfile.
+
+    Returns
+    -------
+    The output file will be in the same folder as the input file with the same name with \"v2\" added
+    
+    '''
+
+    try:
+        file_in = h5py.File(filename_in, 'r')
+    except IOError:
+        print('cannot open ' + filename_in)
+        exit()
+
+    # read data from file
+    data = file_in['data'][:]
+    itermap = file_in['itermap'][:]
+    ntracks = file_in.attrs['NTRACKS'][0]
+    niter = file_in.attrs['NITER'][0]
+    quants = file_in.attrs['QUANTS'][:]
+    file_in_attr_keys = file_in.attrs.keys()
+    sim_attr_keys = file_in['SIMULATION'].attrs.keys()
+    nquants = len(quants)
+
+	# construct file out for new format
+    filename_out = filename_in[:-3] + '-v2' + filename_in[-3:]
+    file_out = h5py.File(filename_out,'w')
+
+	# copy attrs from file_in
+    for item in file_in_attr_keys:
+        file_out.attrs[item] = file_in.attrs[item]
+    for item in sim_attr_keys:
+        file_out.attrs[item] = file_in['SIMULATION'].attrs[item]
+
+    # first pass -- find total size of each track
+    #----------------------------------------#
+    sizes = np.zeros(ntracks)
+
+    itermapshape = itermap.shape
+    for i in range(itermapshape[0]):
+        part_number,npoints,nstart = itermap[i,:]
+        sizes[part_number-1] += npoints
+
+    # initialize ordered data buffer
+    #----------------------------------------#
+    ordered_data = []
+    for i in range(ntracks):
+        ordered_data.append(np.zeros((int(sizes[i]),nquants)))
+    #----------------------------------------#
+
+
+
+    # assign tracks to ordered data from file_in data
+    #----------------------------------------#
+    track_indices = np.zeros(ntracks)
+    data_index = 0
+
+    for i in range(itermapshape[0]):
+        part_number,npoints,nstart = itermap[i,:]
+        track_index =  int(track_indices[part_number-1])
+
+
+        ordered_data[part_number-1][track_index : track_index + npoints,0] \
+        = nstart + np.arange(npoints) * niter
+
+        ordered_data[part_number-1][track_index : track_index + npoints,1:] \
+        = data[data_index:data_index + npoints ,:]
+
+        data_index += npoints
+        track_indices[part_number-1] += npoints
+
+	#----------------------------------------#
+
+	# write to file out
+    for i in range(ntracks):
+        group = file_out.create_group(str(i+1))
+        for j in range(nquants):
+            if(j==0):
+                group.create_dataset(quants[j], data=np.array(ordered_data[i][:, j], dtype=int))
+            else:
+                group.create_dataset(quants[j], data=ordered_data[i][:, j])
+
+    file_out.close()
+    file_in.close()
+    print("Track file converted to the old, more readable format: ", filename_out)
+    return filename_out
+
+def create_file_tags(filename, tags_array):
+    '''
+    Function to write a file_tags file from a (number_of_tags, 2) NumPy array of tags.
+    this file is used to choose particles for the OSIRIS track diagnostic.
+
+    Parameters
+    ----------
+    filename : str
+        Path to the output file where tags will be stored.
+    tags_array: np.ndarray
+        shape (number_of_tags, 2), containing particle tags
+    
+    Returns
+    -------
+    file_tags file with path \"filename\" to be used for the OSIRIS track diagnostic.
+    
+    Notes
+    ------
+    The first element of the tag of a particle that is already being tracked is negative,
+        so we apply the absolute function when generating the file
+    
+    '''
+
+    # In case the particles chosen were already being tracked
+    tags_array[:, 0] = np.abs(tags_array[:, 0])
+    tags_array = tags_array[np.lexsort((tags_array[:, 1], tags_array[:, 0]))]
+    num_tags = tags_array.shape[0]
+    
+    with open(filename, 'w') as file:
+        file.write("! particle tag list\n")
+        file.write(f"! generated on {datetime.now().strftime('%a %b %d %H:%M:%S %Y')}\n")
+        file.write("! number of tags\n")
+        file.write(f"       {num_tags}\n")
+        file.write("! particle tag list\n")
+        
+        for i in range(num_tags):
+            file.write(f"         {tags_array[i, 0]:<6}{tags_array[i, 1]:>6}\n")
+    return filename

{osiris_utils-1.1.3.dist-info → osiris_utils-1.1.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: osiris_utils
-Version: 1.1.3
+Version: 1.1.6
 Summary: Utilities to manipulate and visualize OSIRIS framework output data
 Author: ['João Pedro Ferreira Biu', 'João Cândido', 'Diogo Carvalho']
 Author-email: ['joaopedrofbiu@tecnico.ulisboa.pt']
@@ -19,7 +19,7 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering
-Requires-Python: >=3.11
+Requires-Python: >=3.10
 Description-Content-Type: text/x-rst
 License-File: LICENSE.txt
 Requires-Dist: numpy
@@ -48,6 +48,10 @@ OSIRIS_UTILS
 |Pypi|
 
 This package contains a set of utilities to open and analyze OSIRIS output files, using Python. All the methods implemented are fully integrated with `NumPy`, and use `np.ndarray` as the main data structure.
+High-level functions are provided to manipulate data from OSIRIS, from reading the data of the diagnostics, to making post-processing calculations.
+
+All code is written in Python. To contact the dev team, please send an email to João Biu: `joaopedrofbiu@tecnico.ulisboa.pt <mailto:joaopedrofbiu@tecnico.ulisboa.pt>`_.
+The full dev team can be found below in the Authors and Contributors section.
 
 How to install it?
 ------------------
@@ -58,6 +62,12 @@ To install this package, you can use `pip`::
 
 To install it from source, you can clone this repository and run (in the folder containing ``setup.py``)::
 
+    git clone https://github.com/joaopedrobiu6/osiris_utils.git
+    pip install .
+
+Finally, you can install it in editor mode if you want to contribute to the code::
+    
+    git clone https://github.com/joaopedrobiu6/osiris_utils.git
     pip install -e .
 
 Documentation
@@ -69,3 +79,11 @@ The documentation is available at https://osiris-utils.readthedocs.io or via thi
     :target: https://pypi.org/project/osiris-utils/
     :alt: Pypi
 
+.. _authors:
+
+Authors and Contributors
+------------------------
+
+- João Biu
+- João Cândido
+- Diogo Carvalho

osiris_utils-1.1.6.dist-info/RECORD

@@ -0,0 +1,25 @@
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+osiris_utils/utils.py,sha256=zg-5pOVOieVHXYeNWtCq921Q4PmXVArLInJMd8JURpY,8137
+osiris_utils/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+osiris_utils/data/data.py,sha256=u-0qcPXyTK187j8kGHNgTBgJKX90_YA8jUYno87q9n0,25619
+osiris_utils/data/diagnostic.py,sha256=d9xfTTMFq4p5kVirw94Leq2Jak_gGMjw6PHG2PmRUtE,49179
+osiris_utils/data/simulation.py,sha256=bvJ6UHIzUNUWlWqZbeg60i-Dscl7x6MRZXGfsy8xkWE,6878
+osiris_utils/decks/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+osiris_utils/decks/decks.py,sha256=Ug1_fSfZL9iJwn7dnTvHM0k1Zc4kGpI427QvO0V2pwg,10173
+osiris_utils/decks/species.py,sha256=uZA1oMSltofc2m1s3rK__wjxXfTAQ_3wB2aKRG_PmKo,1066
+osiris_utils/gui/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+osiris_utils/gui/gui.py,sha256=s4not0GzHI3CrA4uQVnjt9jFavkVAeGbQ6rJpM4jir4,10538
+osiris_utils/postprocessing/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+osiris_utils/postprocessing/derivative.py,sha256=p1jhy0Ey8w-AYLVBVGgjpYw19cmLPYV_gdRMHtNSR7w,9602
+osiris_utils/postprocessing/fft.py,sha256=Hif7nQN9RcnpnD_MKxvK5K6DgmINSjgmgYcktIrKdo8,9037
+osiris_utils/postprocessing/field_centering.py,sha256=1i6Fue9PhuED2VxBUq1ggHO3MTSlXjhkFvqh1pb_-Y0,6788
+osiris_utils/postprocessing/heatflux_correction.py,sha256=5_XaDGdB5xP8gDJF9MVIlHN5tggbYHWBgetQvEmAnKQ,7055
+osiris_utils/postprocessing/mft.py,sha256=Ryx0DW8Mb7f0ikf2HfM_T_m2WqrCgcEkMJNZBLZ5qAY,12399
+osiris_utils/postprocessing/mft_for_gridfile.py,sha256=ZaLgwsND9nbD-v-JfCZYxh7-dz3RA-IILwBjZnZGCiE,1522
+osiris_utils/postprocessing/postprocess.py,sha256=f2ZXLnAvLpsLFd-Pygb_sYxwkU4zn1OoF_byVKYAPII,1115
+osiris_utils/postprocessing/pressure_correction.py,sha256=9ZK6BTaGAa8W1ltpXsQf6aTH-xfYJ38076gJToxUFgQ,6345
+osiris_utils-1.1.6.dist-info/licenses/LICENSE.txt,sha256=Cawy2v7wKc7n8yL8guFu-cH9sQw9r1gll1pEFPFAB-Q,1084
+osiris_utils-1.1.6.dist-info/METADATA,sha256=hLLfQtRh4ZEoqt8-LlDHiRg7hU6dWyx65guAXVDu6Fc,3070
+osiris_utils-1.1.6.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+osiris_utils-1.1.6.dist-info/top_level.txt,sha256=mM-_dX5fjzIKB7te655PhZOrPACVY-bJmiASCqW1eOA,13
+osiris_utils-1.1.6.dist-info/RECORD,,

{osiris_utils-1.1.3.dist-info → osiris_utils-1.1.6.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (77.0.3)
+Generator: setuptools (78.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

osiris_utils-1.1.3.dist-info/RECORD

@@ -1,7 +0,0 @@
-osiris_utils/__init__.py,sha256=b41_lLyISC_67CzwRixeSS-MoRog7smLqqfg80XfbbQ,821
-osiris_utils/utils.py,sha256=pj2hrmZla-6T_95eRZB_c4TSXJqBvNRvMTzuw1lPZyA,4708
-osiris_utils-1.1.3.dist-info/licenses/LICENSE.txt,sha256=Cawy2v7wKc7n8yL8guFu-cH9sQw9r1gll1pEFPFAB-Q,1084
-osiris_utils-1.1.3.dist-info/METADATA,sha256=ioKLZT5eREyxC877Fb4FvRRw7Mf2U1a79Dp8PD_fe10,2327
-osiris_utils-1.1.3.dist-info/WHEEL,sha256=1tXe9gY0PYatrMPMDd6jXqjfpz_B-Wqm32CPfRC58XU,91
-osiris_utils-1.1.3.dist-info/top_level.txt,sha256=mM-_dX5fjzIKB7te655PhZOrPACVY-bJmiASCqW1eOA,13
-osiris_utils-1.1.3.dist-info/RECORD,,