From 3d1e69c18148cdf431a1b65ed51492fe384d4c0e Mon Sep 17 00:00:00 2001 From: Axel Huebl Date: Tue, 30 Jan 2018 15:42:04 +0100 Subject: [PATCH] meshesPath & particlesPath: optional Implements that `meshesPath` and `particlesPath` are optional in openPMD 1.1.0+. But if they are set, the directories those attributes point to must exist. --- openpmd_validator/check_h5.py | 94 +++++++++++++++++++++++------------ 1 file changed, 62 insertions(+), 32 deletions(-) diff --git a/openpmd_validator/check_h5.py b/openpmd_validator/check_h5.py index f235a6d..a364a54 100755 --- a/openpmd_validator/check_h5.py +++ b/openpmd_validator/check_h5.py @@ -394,11 +394,13 @@ def check_root_attr(f, v): result_array += test_attr(f, v, "required", "openPMD", np.string_, "^[0-9]+\.[0-9]+\.[0-9]+$") result_array += test_attr(f, v, "required", "openPMDextension", np.uint32) result_array += test_attr(f, v, "required", "basePath", np.string_, "^\/data\/\%T\/$") - result_array += test_attr(f, v, "required", "meshesPath", np.string_) - result_array += test_attr(f, v, "required", "particlesPath", np.string_) result_array += test_attr(f, v, "required", "iterationEncoding", np.string_, "^groupBased|fileBased$") result_array += test_attr(f, v, "required", "iterationFormat", np.string_) + # optional but required for data + result_array += test_attr(f, v, "optional", "meshesPath", np.string_) + result_array += test_attr(f, v, "optional", "particlesPath", np.string_) + # groupBased iteration encoding needs to match basePath if result_array[0] == 0 : if f.attrs["iterationEncoding"].decode() == "groupBased" : @@ -548,35 +550,45 @@ def check_meshes(f, iteration, v, extensionStates): # First element : number of errors # Second element : number of warnings result_array = np.array([ 0, 0]) - + # Find the path to the data base_path = "/data/%s/" % iteration valid, meshes_path = get_attr(f, "meshesPath") - if not valid : - print("Error: `meshesPath` is missing or malformed in '/'") - return( np.array([1, 0]) ) - meshes_path = meshes_path.decode() - - if os.path.join( base_path, meshes_path) != ( base_path + meshes_path ): - print("Error: `basePath`+`meshesPath` seems to be malformed " - "(is `basePath` absolute and ends on a `/` ?)") - return( np.array([1, 0]) ) + if not valid and v: + print("`meshesPath` attribute is missing in '/' " + "(will not search for mesh records)") + meshes_path = None + else: + meshes_path = meshes_path.decode() + + if meshes_path: + if os.path.join( base_path, meshes_path) != ( base_path + meshes_path ): + print("Error: `basePath`+`meshesPath` seems to be malformed " + "(is `basePath` absolute and ends on a `/` ?)") + return( np.array([1, 0]) ) + else: + full_meshes_path = (base_path + meshes_path).encode('ascii') + # if set, a directory must exist with this name + if not full_meshes_path in f: + print("Error: `basePath`+`meshesPath` are set but path '{0}' " + "does not exist in file!".format(full_meshes_path)) + return( np.array([1, 0]) ) + # Find all the meshes + try: + list_meshes = list(f[full_meshes_path].keys()) + except KeyError: + list_meshes = [] + print( "Iteration %s : found %d meshes" + %( iteration, len(list_meshes) ) ) else: - full_meshes_path = (base_path + meshes_path).encode('ascii') - # Find all the meshes - try: - list_meshes = list(f[full_meshes_path].keys()) - except KeyError: - list_meshes = [] - print( "Iteration %s : found %d meshes" - %( iteration, len(list_meshes) ) ) + list_meshes = [] # Check for the attributes of the STANDARD.md for field_name in list_meshes : field = f[full_meshes_path + field_name.encode('ascii')] result_array += test_record(f[full_meshes_path], field_name) - + # General attributes of the record result_array += test_attr(field, v, "required", "unitDimension", np.ndarray, np.float64) @@ -704,18 +716,36 @@ def check_particles(f, iteration, v, extensionStates) : # Find the path to the data base_path = ("/data/%s/" % iteration).encode('ascii') valid, particles_path = get_attr(f, "particlesPath") - if os.path.join( base_path, particles_path) != \ - ( base_path + particles_path ) : - print("Error: `basePath`+`particlesPath` seems to be malformed " - "(is `basePath` absolute and ends on a `/` ?)") - return( np.array([1, 0]) ) + + if not valid and v: + print("`particlesPath` attribute is missing in '/' " + "(will not search for particle records)") + particles_path = None else: - full_particle_path = base_path + particles_path - # Find all the particle species - try: - list_species = list(f[full_particle_path].keys()) - except KeyError: - list_species = [] + particles_path = particles_path.decode() + + if particles_path: + if os.path.join( base_path, particles_path) != \ + ( base_path + particles_path ) : + print("Error: `basePath`+`particlesPath` seems to be malformed " + "(is `basePath` absolute and ends on a `/` ?)") + return(np.array([1, 0])) + else: + full_particle_path = base_path + particles_path + # if set, a directory must exist with this name + if not full_particle_path in f: + print("Error: `basePath`+`particlesPath` are set but path " + "'{0}' does not exist in file!".format( + full_particle_path)) + return(np.array([1, 0])) + # Find all the particle species + try: + list_species = list(f[full_particle_path].keys()) + except KeyError: + list_species = [] + else: + list_species = [] + print( "Iteration %s : found %d particle species" %( iteration, len(list_species) ) )