Modify configuration file. Start estimate_required_memory

nabu/cuda/utils.py

@@ -45,6 +45,15 @@ def count_cuda_devices():
 
 
 
+def get_gpu_memory(device_id):
+    """
+    Return the total memory (in GigaBytes) of a device.
+    """
+    cuda.init()
+    return cuda.Device(device_id).total_memory()/1e9
+
+
+
 """
 pycuda/driver.py
     np.complex64: SIGNED_INT32, num_channels = 2

nabu/resources/cli/reconstruct.py

@@ -12,13 +12,20 @@ The user needs to provide:
 import os
 from .utils import parse_params_values
 from .cli_configs import ReconstructConfig
+from .validate import validate_conffile_noexcept
 
-def parse_args():
+
+def main():
     args = parse_params_values(
         ReconstructConfig,
         parser_description="Perform a tomographic reconstruction."
     )
 
+    validator = validate_conffile_noexcept(args["input_file"], print_ok=False)
+    nabu_config = validator.nabu_config
+    dataset_structure = validator.dataset_config
+
+
 
 if __name__ == "__main__":
-    parse_args()
+    main()

nabu/resources/cli/validate.py

@@ -25,7 +25,7 @@ def get_config(fname):
     return config
 
 
-def nabu_validate(fname):
+def validate_conffile(fname):
     # Read the configuration file and extract the key/values
     config = get_config(fname)
 
@@ -42,6 +42,19 @@ def nabu_validate(fname):
     # Remove unused radios (modifies dataset_structure)
     validator.remove_unused_radios()
 
+    return validator
+
+
+def validate_conffile_noexcept(fname, print_ok=True):
+    try:
+        validator = validate_conffile(fname)
+    except Exception as exc:
+        print("Error while checking %s:" % fname)
+        print(exc)
+        exit(-1)
+    if print_ok:
+        print("Configuration file %s is valid" % fname)
+    return validator
 
 
 def main():
@@ -50,13 +63,7 @@ def main():
         parser_description="Validate a Nabu configuration file."
     )
     fname = args["input_file"]
-    try:
-        nabu_validate(fname)
-    except Exception as exc:
-        print("Error while checking %s:" % fname)
-        print(exc)
-        exit(-1)
-    print("Configuration file %s is valid" % fname)
+    validate_conffile_noexcept(fname)
 
 if __name__ == "__main__":
     main()

nabu/resources/computations.py

+#!/usr/bin/env python
+
+"""
+computations.py: determine computational needs, chunking method to be used, etc.
+"""
+
+
+
+
+
+def get_chunk_size(nabu_config, dataset, available_mem):
+    """
+    Return the maximum chunk size that can be used with a given amount of memory.
+    """
+
+
+
+
+def estimate_required_memory(nabu_config, dataset, chunk_size=None):
+    """
+    Estimate the memory (RAM) needed for a reconstruction.
+
+    Parameters
+    ----------
+    nabu_config: dict
+        Dictionary describing the nabu configuration. Usually extracted from
+        the configuration file.
+    dataset: nabu.resources.dataset_analyzer.DatasetAnalyzer
+        Dataset structure.
+    """
+
+    Ny, Nx = dataset.radio_dims
+    Na = dataset.n_angles
+    if chunk_size is not None:
+        Ny = chunk_size
+    if nabu_config["dataset"]["binning"]:
+        Nx = Nx // nabu_config["dataset"]["binning"]
+    if nabu_config["dataset"]["binning_z"]:
+        Ny = Ny // nabu_config["dataset"]["binning_z"]
+    if nabu_config["dataset"]["projections_subsampling"]:
+        Na = Na // nabu_config["dataset"]["projections_subsampling"]
+
+    data_volume_size = Nx * Ny * Na * 2 # assuming uint16
+
+
+    rec_config = nabu_config["reconstruction"]
+    reconstructed_volume_size = 0
+    if rec_config["method"] != "none":
+        Nx_rec = rec_config["end_x"] - rec_config["start_x"] + 1
+        Ny_rec = rec_config["end_y"] - rec_config["start_y"] + 1
+        Nz_rec = rec_config["end_z"] - rec_config["start_z"] + 1
+        reconstructed_volume_size = Nx_rec * Ny_rec * Nz_rec * 4 # float32
+

nabu/resources/nabu_config.py

@@ -46,6 +46,24 @@ nabu_config = {
             "hst_key": "background_file",
             "validator": optional_file_name_validator,
         },
+        "binning": {
+            "default": "1",
+            "help": "Binning factor.\nThe final slices dimensions will be divided by 'slices_binning'",
+            "hst_key": None,
+            "validator": binning_validator,
+        },
+        "binning_z": {
+            "default": "1",
+            "help": "Whether to also bin in the 'z' direction, resulting in a lesser number of reconstructed slices",
+            "hst_key": None,
+            "validator": binning_validator,
+        },
+        "projections_subsampling": {
+            "default": "1",
+            "help": "Projections subsampling factor: take one projection out of 'projection_subsampling'",
+            "hst_key": "file_interval",
+            "validator": binning_validator,
+        },
     },
     "preproc": {
         "flatfield_enabled": {
@@ -162,7 +180,7 @@ nabu_config = {
         },
         "method": {
             "default": "FBP",
-            "help": "Reconstruction method",
+            "help": "Reconstruction method. Possible values: FBP, none. If value is 'none', no reconstruction will be done.",
             "hst_key": None,
             "validator": reconstruction_method_validator,
         },
@@ -220,24 +238,6 @@ nabu_config = {
             "hst_key": None,
             "validator": integer_validator,
         },
-        "slices_binning": {
-            "default": "1",
-            "help": "Binning factor in the case where the reconstructed slices are to be binned.\nThe slices dimensions will be divided by 'slices_binning'",
-            "hst_key": None,
-            "validator": binning_validator,
-        },
-        "slices_binning_z": {
-            "default": "1",
-            "help": "Whether to also bin in the 'z' direction, resulting in a lesser number of reconstructed slices",
-            "hst_key": None,
-            "validator": binning_validator,
-        },
-        "projections_subsampling": {
-            "default": "1",
-            "help": "Projections subsampling factor: take one projection out of 'projection_subsampling'",
-            "hst_key": "file_interval",
-            "validator": binning_validator,
-        },
         "iterations": {
             "default": "200",
             "help": "\nParameters for iterative algorithms\n------------------------------------\nNumber of iterations",

nabu/resources/validators.py

@@ -203,7 +203,7 @@ def padding_mode_validator(val):
 
 @validator
 def reconstruction_method_validator(val):
-    avail_rec_methods = ["fbp", "dfi"]
+    avail_rec_methods = ["fbp", "none"] # dfi, iterative...
     return name_range_checker(val, avail_rec_methods, "reconstruction method")
 
 @validator

setup.py

@@ -109,6 +109,7 @@ def setup_package():
                 "nabu-test=nabu.tests:nabu_test",
                 "nabu-config=nabu.resources.cli.bootstrap:bootstrap",
                 "nabu-validate=nabu.resources.cli.validate:main",
+                "nabu-reconstruct=nabu.resources.cli.reconstruct:main",
             ],
         },