Richardson Lucy Parallelization

cosipy/image_deconvolution/RLparallelscript.py

@@ -0,0 +1,375 @@
+import os
+from pathlib import Path
+import logging
+import argparse
+
+# logging setup
+logger = logging.getLogger(__name__)
+
+# argparse setup
+parser = argparse.ArgumentParser()
+parser.add_argument("--numrows", type=int, dest='numrows', help="Number of rows in the response matrix")
+parser.add_argument("--numcols", type=int, dest='numcols', help="Number of columns in the response matrix")
+parser.add_argument("--base_dir", type=str, dest='base_dir', help="Current working directory and where configuration file is assumed to lie")
+parser.add_argument("--config_file", type=str, dest='config_file', help="Name of configuration file (assumed to lie in CWD)")
+args = parser.parse_args()
+
+# Import third party libraries
+import numpy as np
+from mpi4py import MPI
+import h5py
+from yayc import Configurator
+
+# Load configuration file
+config = Configurator.open(f'{args.base_dir}/{args.config_file}')
+
+# Number of elements in data space (ROWS) and model space (COLS)
+NUMROWS = args.numrows        # TODO: Ideally, for row-major form to exploit caching, NUMROWS must be smaller than NUMCOLS
+NUMCOLS = args.numcols
+
+# Define MPI and iteration misc variables
+MASTER = 0                      # Indicates master process
+MAXITER = config.get('deconvolution:parameter:iteration_max', 10)
+
+# FILE_DIR = Path(os.path.dirname(os.path.abspath(__file__)))
+BASE_DIR = Path(args.base_dir)
+RESULTS_DIR = BASE_DIR / config.get('deconvolution:parameter:save_results_directory', './results')
+
+'''
+Response matrix
+'''
+def load_response_matrix(comm, start_row, end_row, filename='response_matrix.h5'):
+    with h5py.File(BASE_DIR / filename, "r", driver="mpio", comm=comm) as f1:
+        dataset = f1["response_matrix"]
+        R = dataset[start_row:end_row, :]
+    return R
+
+'''
+Response matrix transpose
+'''
+def load_response_matrix_transpose(comm, start_col, end_col, filename='response_matrix.h5'):
+    with h5py.File(BASE_DIR / filename, "r", driver="mpio", comm=comm) as f1:
+        dataset = f1["response_matrix"]
+        RT = dataset[:, start_col:end_col]
+    return RT
+
+'''
+Response matrix summed along axis=i
+'''
+def load_axis0_summed_response_matrix(filename='response_matrix.h5'):
+    with h5py.File(BASE_DIR / filename, "r") as f1:
+        dataset = f1["response_vector"]
+        Rj = dataset[:]
+    return Rj
+
+'''
+Sky model
+'''
+def initial_sky_model(model_init_val=[1e-4]):
+    M0 = np.ones(NUMCOLS, dtype=np.float64) * float(model_init_val[0])     # Initial guess according to image_deconvolution.py. TODO: Make this more general than element 0
+    return M0
+
+'''
+Background model
+'''
+def load_bg_model(filename='bg.csv'):
+    bg = np.loadtxt(filename)
+    return bg
+
+'''
+Observed data
+'''
+def load_event_data(filename='event.csv'):
+    event = np.loadtxt(filename)
+    return event
+
+def register_result(iter, M, delta):
+    """
+    The values below are stored at the end of each iteration.
+    - iteration: iteration number
+    - model: updated image
+    - delta_model: delta map after M-step 
+    - processed_delta_model: delta map after post-processing
+    - alpha: acceleration parameter in RL algirithm
+    - background_normalization: optimized background normalization
+    - loglikelihood: log-likelihood
+    """
+
+    this_result = {"iteration": iter, 
+                    "model": M, 
+                    "delta_model": delta,
+                    # "processed_delta_model": copy.deepcopy(self.processed_delta_model), TODO: The RL parallel implementation does not currently support smooth convergence through weighting, background normalization, or likelihood calculation
+                    # "background_normalization": copy.deepcopy(self.dict_bkg_norm),
+                    # "alpha": self.alpha, 
+                    # "loglikelihood": copy.deepcopy(self.loglikelihood_list)
+                    }
+
+    # # show intermediate results
+    # logger.info(f'  alpha: {this_result["alpha"]}')
+    # logger.info(f'  background_normalization: {this_result["background_normalization"]}')
+    # logger.info(f'  loglikelihood: {this_result["loglikelihood"]}')
+
+    return this_result
+
+def save_results(results):
+    '''
+    NOTE: Copied from RichardsonLucy.py
+    '''
+    logger.info('Saving results in {RESULTS_DIR}')
+    # model
+    for this_result in results:
+        iteration_count = this_result["iteration"]
+        # this_result["model"].write(f"{RESULTS_DIR}/model_itr{iteration_count}.hdf5", overwrite = True)    # TODO: numpy arrays do not support write_to_hdf5 as a method. Need to ensure rest of code is modified to support cosipy.image_deconvolution.allskyimage.AllSkyImageModel
+        # this_result["delta_model"].write(f"{RESULTS_DIR}/delta_model_itr{iteration_count}.hdf5", overwrite = True)
+        # this_result["processed_delta_model"].write(f"{RESULTS_DIR}/processed_delta_model_itr{iteration_count}.hdf5", overwrite = True)    TODO: processed_delta_model here is not different from delta_model
+        np.savetxt(f'{RESULTS_DIR}/model_itr{iteration_count}.csv', this_result['model'], delimiter=',')
+        np.savetxt(f'{RESULTS_DIR}/delta_model_itr{iteration_count}.csv', this_result['delta_model'], delimiter=',')
+
+    # TODO: The following will be enabled once the respective calculations are incorporated
+    # #fits
+    # primary_hdu = fits.PrimaryHDU()
+
+    # col_iteration = fits.Column(name='iteration', array=[float(result['iteration']) for result in self.results], format='K')
+    # col_alpha = fits.Column(name='alpha', array=[float(result['alpha']) for result in self.results], format='D')
+    # cols_bkg_norm = [fits.Column(name=key, array=[float(result['background_normalization'][key]) for result in self.results], format='D') 
+    #                 for key in self.dict_bkg_norm.keys()]
+    # cols_loglikelihood = [fits.Column(name=f"{self.dataset[i].name}", array=[float(result['loglikelihood'][i]) for result in self.results], format='D') 
+    #                     for i in range(len(self.dataset))]
+
+    # table_alpha = fits.BinTableHDU.from_columns([col_iteration, col_alpha])
+    # table_alpha.name = "alpha"
+
+    # table_bkg_norm = fits.BinTableHDU.from_columns([col_iteration] + cols_bkg_norm)
+    # table_bkg_norm.name = "bkg_norm"
+
+    # table_loglikelihood = fits.BinTableHDU.from_columns([col_iteration] + cols_loglikelihood)
+    # table_loglikelihood.name = "loglikelihood"
+
+    # hdul = fits.HDUList([primary_hdu, table_alpha, table_bkg_norm, table_loglikelihood])
+    # hdul.writeto(f'{RESULTS_DIR}/results.fits',  overwrite=True)
+
+def main():
+    # Set up MPI
+    comm = MPI.COMM_WORLD
+    numtasks = comm.Get_size()
+    taskid = comm.Get_rank()
+
+    # Calculate the indices in Rij that the process has to parse. My hunch is that calculating these scalars individually will be faster than the MPI send broadcast overhead.
+    averow = NUMROWS // numtasks
+    extra_rows = NUMROWS % numtasks
+    start_row = taskid * averow
+    end_row = (taskid + 1) * averow if taskid < (numtasks - 1) else NUMROWS
+
+    # Calculate the indices in Rji, i.e., Rij transpose, that the process has to parse.
+    avecol = NUMCOLS // numtasks
+    extra_cols = NUMCOLS % numtasks
+    start_col = taskid * avecol
+    end_col = (taskid + 1) * avecol if taskid < (numtasks - 1) else NUMCOLS
+
+    # Initialise vectors required by all processes
+    epsilon = np.zeros(NUMROWS)                 # All gatherv-ed. Explicit variable declaration.
+    epsilon_fudge = 1e-12                       # To prevent divide-by-zero and underflow errors. Value taken from `almost_zero = 1e-12` in dataIF_COSI_DC2.py
+
+    # Initialise epsilon_slice and C_slice. Explicit variable declarations. 
+    epsilon_slice = np.zeros(end_row - start_row)
+    C_slice = np.zeros(end_col - start_col)
+
+    # Load R and RT into memory (single time if response matrix doesn't 
+    # change with time)
+    R = load_response_matrix(comm, start_row, end_row)
+    RT = load_response_matrix_transpose(comm, start_col, end_col)
+
+    # Loaded and broadcasted by master.
+    M = np.empty(NUMCOLS, dtype=np.float64) 
+    d = np.empty(NUMROWS, dtype=np.float64)  
+    bg = np.zeros(NUMROWS)                  
+
+# ****************************** MPI ******************************
+
+# **************************** Part I *****************************
+
+    '''*************** Master ***************'''
+
+    if taskid == MASTER:
+
+        # Pretty print definitions
+        linebreak_stars = '**********************'
+        linebreak_dashes = '----------------------'
+
+        # Log input information (Only master node does this)
+        save_results_flag = config.get('deconvolution:parameter:save_results', False)       # Extract from config file
+        logger.info(linebreak_stars)
+        logger.info(f'Number of elements in data space: {NUMROWS}')
+        logger.info(f'Number of elements in model space: {NUMCOLS}')
+        logger.info(f'Base directory: {BASE_DIR}')
+        if save_results_flag == True:
+            logger.info(f'Results directory (if save_results flag is set to True): {RESULTS_DIR}')
+        logger.info(f'Configuration filename: {args.config_file}')
+        logger.info(f'Master node: {MASTER}')
+        logger.info(f'Maximum number of RL iterations: {MAXITER}')
+
+        # Load Rj vector (response matrix summed along axis=i)
+        Rj = load_axis0_summed_response_matrix()
+
+        # Generate initial sky model from configuration file
+        M = initial_sky_model(model_init_val=config.get('model_definition:initialization:parameter:value', [1e-4]))
+
+        # Load event data and background model (intermediate files created in RichardsonLucyParallel.py)
+        bg = load_bg_model()
+        d = load_event_data()
+
+        # Sanity check: print d
+        print()
+        print('Observed data-space d vector:')
+        print(d)
+        ## Pretty print
+        print()
+        print(linebreak_stars)
+
+        # Initialise C vector. Only master requires full length. Explicit variable declaration.
+        C = np.empty(NUMCOLS, dtype=np.float64)
+
+        # Initialise update delta vector. Explicit variable declaration.
+        delta = np.empty(NUMCOLS, dtype=np.float64)
+
+        # Initialise list for results. See function register_result() for list elements. 
+        results = []
+
+    '''*************** Worker ***************'''
+
+    if taskid > MASTER:
+        # Only separate if... clause for NON-MASTER processes. 
+        # Initialise C vector to None. Only master requires full length.
+        C = None
+
+    # Broadcast d vector
+    comm.Bcast([d, MPI.DOUBLE], root=MASTER)
+
+    # Scatter bg vector to epsilon_BG
+    comm.Bcast([bg, MPI.DOUBLE], root=MASTER)
+    # comm.Scatter(bg, [epsilon_BG, recvcounts, displacements, MPI.DOUBLE])
+
+    # print(f"TaskID {taskid}, gathered broadcast")
+
+    # Sanity check: print epsilon
+    # if taskid == MASTER:
+    #     print('epsilon_BG')
+    #     print(bg)
+    #     print()
+
+# **************************** Part IIa *****************************
+
+    '''***************** Begin Iterative Segment *****************'''
+    # Set up initial values for iterating variables.
+    # Exit if:
+    ## 1. Max iterations are reached
+    # for iter in tqdm(range(MAXITER)):
+    for iter in range(MAXITER):
+
+        '''*************** Master ***************'''
+        if taskid == MASTER:
+            # Pretty print - starting
+            print(f"Starting iteration {iter + 1}")
+            # logger.info(f"## Iteration {self.iteration_count}/{self.iteration_max} ##")
+            # logger.info("<< E-step >>")
+
+
+    # Calculate epsilon vector and all gatherv
+
+        '''**************** All *****************'''
+
+        '''Synchronization Barrier 1'''
+        # Broadcast M vector
+        comm.Bcast([M, MPI.DOUBLE], root=MASTER)
+
+        # Calculate epsilon slice
+        epsilon_BG = bg[start_row:end_row]             # TODO: Change the way epsilon_BG is loaded. Make it taskID dependent through MPI.Scatter for example. Use `recvcounts`
+        epsilon_slice = np.dot(R, M) + epsilon_BG + epsilon_fudge   # TODO: For a more general implementation, see calc_expectation() in dataIF_COSI_DC2.py
+
+        '''Synchronization Barrier 2'''
+        # All vector gather epsilon slices
+        recvcounts = [averow] * (numtasks-1) + [averow + extra_rows]
+        displacements = np.arange(numtasks) * averow
+        comm.Allgatherv(epsilon_slice, [epsilon, recvcounts, displacements, MPI.DOUBLE])
+
+        # Sanity check: print epsilon
+        # if taskid == MASTER:
+        #     print('epsilon')
+        #     print(epsilon)
+        #     print(epsilon.min(), epsilon.max())
+        #     print()
+
+# **************************** Part IIb *****************************
+
+    # Calculate C vector and gatherv
+
+        '''**************** All *****************'''
+
+        # Calculate C slice
+        C_slice = np.dot(RT.T, d/epsilon)
+
+        '''Synchronization Barrier 3'''
+        # All vector gather C slices
+        recvcounts = [avecol] * (numtasks-1) + [avecol + extra_cols]
+        displacements = np.arange(numtasks) * avecol
+        comm.Gatherv(C_slice, [C, recvcounts, displacements, MPI.DOUBLE], root=MASTER)
+
+# **************************** Part IIc *****************************
+
+    # Iterative update of model-space M vector
+
+        if taskid == MASTER:
+
+            # logger.info("<< M-step >>")
+
+            # Sanity check: print C
+            # print('C')
+            # print(C)
+            # print(C.min(), C.max())
+            # print()
+
+            delta = C / Rj - 1
+            M = M + delta * M           # Allows for optimization features presented in Siegert et al. 2020
+
+            # Sanity check: print M
+            # print('M')
+            # print(np.round(M, 5))
+            # print(np.round(M.max(), 5))
+
+            # Sanity check: print delta
+            # print('delta')
+            # print(delta)
+
+            # Pretty print - completion
+            print(f"Done")
+            print(linebreak_dashes)
+
+            # Save iteration
+            if save_results_flag == True:
+                results.append(register_result(iter, M, delta))
+
+    '''****************** End Iterative Segment ******************'''
+
+    # Print converged M
+    if taskid == MASTER:
+        # logger.info("<< Registering Result >>")
+        print('Converged M vector:')
+        print(np.round(M, 5))
+        print(np.round(M.max(), 5))
+        print(np.sum(M))
+        print()
+
+        if save_results_flag == True:
+            save_results(results)
+
+        # MAXITER
+        if iter == (MAXITER - 1):
+            print(f'Reached maximum iterations = {MAXITER}')
+            print(linebreak_stars)
+            print()
+
+    # MPI Shutdown
+    MPI.Finalize()
+
+if __name__ == "__main__":
+    main()

cosipy/image_deconvolution/RichardsonLucy.py

@@ -36,7 +36,7 @@ class RichardsonLucy(DeconvolutionAlgorithmBase):
 
     """
 
-    def __init__(self, initial_model, dataset, mask, parameter):
+    def __init__(self, initial_model, dataset, mask, parameter, parameter_filepath = None):
 
         DeconvolutionAlgorithmBase.__init__(self, initial_model, dataset, mask, parameter)