Merge pull request #100 from RemiLehe/fix_check_all_files

Close #98 : `check_all_files=False` breaks slider and time access of data

opmd_viewer/openpmd_timeseries/data_reader/params_reader.py

@@ -14,7 +14,7 @@
 from .utilities import is_scalar_record, get_shape, get_bpath
 
 
-def read_openPMD_params(filename):
+def read_openPMD_params(filename, extract_parameters=True):
     """
     Extract the time and some openPMD parameters from a file
 
@@ -23,14 +23,17 @@ def read_openPMD_params(filename):
     filename: string
         The path to the file from which parameters should be extracted
 
+    extract_parameters: bool, optional
+        Whether to extract all parameters or only the time
+        (Function execution is faster when extract_parameters is False)
+
     Returns
     -------
     A tuple with:
     - A float corresponding to the time of this iteration in SI units
     - A dictionary containing several parameters, such as the geometry, etc.
+      When extract_parameters is False, the second argument returned is None.
     """
-    params = {}
-
     # Open the file, and do a version check
     f = h5py.File(filename, 'r')
     version = f.attrs['openPMD'].decode()
@@ -39,6 +42,17 @@ def read_openPMD_params(filename):
             "File %s is not supported: Invalid openPMD version: "
             "%s)" % (filename, version))
 
+    # Find the base path object, and extract the time
+    bpath = f[get_bpath(f)]
+    t = bpath.attrs["time"] * bpath.attrs["timeUnitSI"]
+
+    # If the user did not request more parameters, exit now.
+    if not extract_parameters:
+        return(t, None)
+
+    # Otherwise, extract the rest of the parameters
+    params = {}
+
     # Find out supported openPMD extensions claimed by this file
     # note: a file might implement multiple extensions
     known_extensions = {'ED-PIC': np.uint32(1)}
@@ -53,10 +67,6 @@ def read_openPMD_params(filename):
         if bitmask_all_extensions & bitmask == bitmask:
             params['extensions'].append(extension)
 
-    # Find the base path object, and extract the time
-    bpath = f[get_bpath(f)]
-    t = bpath.attrs["time"] * bpath.attrs["timeUnitSI"]
-
     # Find out whether fields are present and extract their geometry
     meshes_path = f.attrs['meshesPath'].decode().strip('/')
     if meshes_path in bpath.keys():

opmd_viewer/openpmd_timeseries/main.py

@@ -31,20 +31,16 @@
           'The opmd_viewer API is nonetheless working.')
     parent_class = object
 
-# Define a custom Exception
-
 
+# Define a custom Exception
 class OpenPMDException(Exception):
-
     "Exception raised for invalid use of the openPMD-viewer API"
     pass
 
+
 # Define the OpenPMDTimeSeries class and have it inherit
 # from the parent class defined above
-
-
 class OpenPMDTimeSeries(parent_class):
-
     """
     Main class for the exploration of an openPMD timeseries
 
@@ -100,19 +96,19 @@ def __init__(self, path_to_dir, check_all_files=True):
         self.avail_species = params0['avail_species']
         self.avail_record_components = \
             params0['avail_record_components']
-        # deprecated
-        self.avail_ptcl_quantities = params0['avail_ptcl_quantities']
-
-        # - Check that the other files have the same parameters
-        if check_all_files:
-            for k in range(1, N_files):
-                t, params = read_openPMD_params(self.h5_files[k])
-                self.t[k] = t
+
+        # - Extract the time for each file and, if requested, check
+        #   that the other files have the same parameters
+        for k in range(1, N_files):
+            t, params = read_openPMD_params(self.h5_files[k], check_all_files)
+            self.t[k] = t
+            if check_all_files:
                 for key in params0.keys():
                     if params != params0:
                         print("Warning: File %s has different openPMD "
                               "parameters than the rest of the time series."
                               % self.h5_files[k])
+                        break
 
         # - Set the current iteration and time
         self.current_i = 0