import numpy as np
from ...errors import MissingMetaDataError
from ...lazy_loader import LazyData
from ...meta import LazyMetaValue
from .jpk_reader import JPKReader
__all__ = ["load_jpk"]
def detect(path, return_modality=False):
"""Check whether a file is a valid JPK data file
"""
# The suffix is not checked, because that is done in
# the wrapper class formats.AFMFormatRecipe.
jpkr = JPKReader(path)
try:
jpkr.get_metadata(index=0)
except MissingMetaDataError:
valid = True
except BaseException:
valid = False
else:
valid = True
if return_modality:
return valid, jpkr.get_imaging_mode()
else:
return valid
[docs]def load_jpk(path, callback=None, meta_override=None):
"""Loads JPK Instruments data files
These files are zip files containing java property files and
integer-encoded binary data. The property files include recipes
on how to convert the raw integer data to SI units.
Parameters
----------
path: str or pathlib.Path
path to JPK data file
callback: callable
function for progress tracking; must accept a float in
[0, 1] as an argument.
meta_override: dict
if specified, contains key-value pairs of metadata that
are used when loading the files
(see :data:`afmformats.meta.META_FIELDS`)
"""
if meta_override is None:
meta_override = {}
jpkr = JPKReader(path)
jpkr.set_metadata(meta_override)
dataset = []
# iterate over all datasets and add them
for index in range(len(jpkr)):
lazy_data = LazyData()
for column in ["force", "height (measured)", "height (piezo)",
"segment", "time"]:
lazy_data.set_lazy_loader(column=column,
func=jpkr.get_data,
kwargs={"column": column,
"index": index})
metadata = jpkr.get_metadata(index=index)
metadata["z range"] = LazyMetaValue(
lambda data: np.ptp(data["height (piezo)"]),
lazy_data)
dataset.append({"data": lazy_data,
"metadata": metadata,
})
if callback:
callback((1+index) / len(jpkr))
return dataset
recipe_jpk_force = {
"descr": "binary FD data",
"detect": detect,
"loader": load_jpk,
"maker": "JPK Instruments",
"modalities": ["creep-compliance", "force-distance", "stress-relaxation"],
"suffix": ".jpk-force",
}
recipe_jpk_force_map = {
"descr": "binary QMap data",
"detect": detect,
"loader": load_jpk,
"maker": "JPK Instruments",
"modalities": ["creep-compliance", "force-distance", "stress-relaxation"],
"suffix": ".jpk-force-map",
}
recipe_jpk_force_qi_data = {
"descr": "binary QMap data",
"detect": detect,
"loader": load_jpk,
"maker": "JPK Instruments",
"modalities": ["creep-compliance", "force-distance", "stress-relaxation"],
"suffix": ".jpk-qi-data",
}
recipe_jpk_force_qi_series = {
"descr": "binary QMap data",
"detect": detect,
"loader": load_jpk,
"maker": "JPK Instruments",
"modalities": ["creep-compliance", "force-distance", "stress-relaxation"],
"suffix": ".jpk-qi-series",
}