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New Attribute: speciesType #38

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merged 3 commits into from
Apr 3, 2018
Merged

New Attribute: speciesType #38

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New Attribute: speciesType
ax3l Apr 3, 2018
386fd88
Example: SpeciesType
ax3l Apr 3, 2018
71f9705
Regex Comments
ax3l Apr 3, 2018
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42 changes: 34 additions & 8 deletions openpmd_validator/check_h5.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,13 +26,14 @@
# version of the openPMD standard
openPMD = "2.0.0"

ext_list = ["ED-PIC"]
ext_list = ["ED-PIC", "SpeciesType"]

def help():
""" Print usage information for this file """
print('This is the openPMD file check for HDF5 files.\n')
print('Check for format version: %s\n' % openPMD)
print('Usage:\n checkOpenPMD_h5.py -i <fileName> [-v] [--EDPIC]')
print('Usage:\n checkOpenPMD_h5.py -i <fileName> [-v] [--EDPIC] '
'[--SpeciesType]')
sys.exit()


Expand All @@ -41,8 +42,10 @@ def parse_cmd(argv):
file_name = ''
verbose = False
force_extension_pic = False
force_extension_speciestype = False
try:
opts, args = getopt.getopt(argv,"hvi:e",["file=","EDPIC"])
opts, args = getopt.getopt(argv,"hvi:e",
["file=","EDPIC", "SpeciesType"])
except getopt.GetoptError:
print('checkOpenPMD_h5.py -i <fileName>')
sys.exit(2)
Expand All @@ -53,12 +56,14 @@ def parse_cmd(argv):
verbose = True
elif opt in ("--EDPIC"):
force_extension_pic = True
elif opt in ("--SpeciesType"):
force_extension_speciestype = True
elif opt in ("-i", "--file"):
file_name = arg
if not os.path.isfile(file_name):
print("File '%s' not found!" % file_name)
help()
return(file_name, verbose, force_extension_pic)
return file_name, verbose, force_extension_pic, force_extension_speciestype


def open_file(file_name):
Expand Down Expand Up @@ -392,7 +397,7 @@ def check_root_attr(f, v):
result_array += test_attr(f, v, "required", "iterationFormat", np.string_)

# optional but required for extensions
result_array += test_attr(f, v, "optional", "openPMDextension", np.string_, "^[a-zA-Z0-9-;]+$")
result_array += test_attr(f, v, "optional", "openPMDextension", np.string_, "^[a-zA-Z0-9\-;]+$")
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@ax3l ax3l Apr 3, 2018 •
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note: this is a bug-fix for extension names from the last PR. The - needs an escape, otherwise it's a regex range.
(\ is not allowed, would also need an escape.)

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Since regex can sometimes be cryptic, would you add a comment explaining what it does? Like

# Check that openPMDextension contains only letters, or digits, or the characters `-` and `;`

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yes, great point!

# 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_)
Expand Down Expand Up @@ -677,6 +682,16 @@ def check_meshes(f, iteration, v, extensionStates):
if (valid == True) and (field_smoothing != b"none") :
result_array += test_attr(field,v, "required",
"fieldSmoothingParameters", np.string_)

# Check the attributes in the SpeciesType extension
if extensionStates['SpeciesType'] :
# Check for the attributes of each record
for field_name in list_meshes :
field = f[full_meshes_path + field_name.encode('ascii')]
result_array += test_attr(field, v, "optional",
"speciesType", np.string_,
"^[a-zA-Z0-9\-;:]+$")

return(result_array)


Expand Down Expand Up @@ -824,6 +839,11 @@ def check_particles(f, iteration, v, extensionStates) :
result_array += test_attr(species, v, "required",
"particleSmoothingParameters", np.string_)

# Check the attributes associated with the SpeciesType extension
if extensionStates['SpeciesType'] :
result_array += test_attr(species, v, "optional", "speciesType",
np.string_, "^[a-zA-Z0-9\-;:]+$")

# Check attributes of each record of the particle
for record in list(species.keys()) :
# all records (but particlePatches) require units
Expand Down Expand Up @@ -851,7 +871,8 @@ def check_particles(f, iteration, v, extensionStates) :
return(result_array)


def check_file(file_name, verbose=False, force_extension_pic=False):
def check_file(file_name, verbose=False, force_extension_pic=False,
force_extension_speciestype=False):
f = open_file(file_name)

# root attributes at "/"
Expand All @@ -862,6 +883,9 @@ def check_file(file_name, verbose=False, force_extension_pic=False):
if force_extension_pic and not extensionStates["ED-PIC"] :
print("Error: Extension `ED-PIC` not found in file!")
result_array += np.array([1, 0])
if force_extension_speciestype and not extensionStates["SpeciesType"] :
print("Error: Extension `SpeciesType` not found in file!")
result_array += np.array([1, 0])

# Go through all the iterations, checking both the particles
# and the meshes
Expand All @@ -871,8 +895,10 @@ def check_file(file_name, verbose=False, force_extension_pic=False):


def main():
file_name, verbose, force_extension_pic = parse_cmd(sys.argv[1:])
result_array = check_file(file_name, verbose, force_extension_pic)
file_name, verbose, \
force_extension_pic, force_extension_speciestype = parse_cmd(sys.argv[1:])
result_array = check_file(file_name, verbose,
force_extension_pic, force_extension_speciestype)

# results
print("Result: %d Errors and %d Warnings."
Expand Down
6 changes: 4 additions & 2 deletions openpmd_validator/createExamples_h5.py
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Original file line number Diff line number Diff line change
Expand Up @@ -88,8 +88,8 @@ def setup_root_attr(f):
The file in which to write the data
"""

# extensions list: ED-PIC extension is used
ext_list = ["ED-PIC"]
# extensions list: ED-PIC and SpeciesType extensions are used
ext_list = ["ED-PIC", "SpeciesType"]

# Required attributes
f.attrs["openPMD"] = np.string_("2.0.0")
Expand Down Expand Up @@ -139,6 +139,7 @@ def write_rho_cylindrical(meshes, mode0, mode1):
rho = meshes[full_rho_path]
rho.attrs["comment"] = np.string_(
"Density of electrons in azimuthal decomposition")
rho.attrs["speciesType"] = np.string_("electron")

# Create the dataset (cylindrical with azimuthal modes up to m=1)
# The first axis has size 2m+1
Expand Down Expand Up @@ -323,6 +324,7 @@ def add_EDPIC_attr_particles(particle):
The group of the particle that gets additional attributes.

"""
particle.attrs["speciesType"] = np.string_("electron")
particle.attrs["particleShape"] = 3.0
particle.attrs["currentDeposition"] = np.string_("Esirkepov")
# particle.attrs["currentDepositionParameters"] = np.string_("")
Expand Down