diff options
Diffstat (limited to 'src/silx/io/fioh5.py')
| -rw-r--r-- | src/silx/io/fioh5.py | 200 |
1 files changed, 116 insertions, 84 deletions
diff --git a/src/silx/io/fioh5.py b/src/silx/io/fioh5.py index 0a86bbf..a88d35b 100644 --- a/src/silx/io/fioh5.py +++ b/src/silx/io/fioh5.py @@ -154,15 +154,17 @@ logger1 = logging.getLogger(__name__) if h5py.version.version_tuple[0] < 3: text_dtype = h5py.special_dtype(vlen=str) # old API else: - text_dtype = 'O' # variable-length string (supported as of h5py > 3.0) + text_dtype = "O" # variable-length string (supported as of h5py > 3.0) ABORTLINENO = 5 -dtypeConverter = {'STRING': text_dtype, - 'DOUBLE': 'f8', - 'FLOAT': 'f4', - 'INTEGER': 'i8', - 'BOOLEAN': '?'} +dtypeConverter = { + "STRING": text_dtype, + "DOUBLE": "f8", + "FLOAT": "f4", + "INTEGER": "i8", + "BOOLEAN": "?", +} def is_fiofile(filename): @@ -192,56 +194,51 @@ def is_fiofile(filename): class FioFile(object): - """This class opens a FIO file and reads the data. - - """ + """This class opens a FIO file and reads the data.""" def __init__(self, filepath): # parse filename filename = os.path.basename(filepath) - fnowithsuffix = filename.split('_')[-1] + fnowithsuffix = filename.split("_")[-1] try: - self.scanno = int(fnowithsuffix.split('.')[0]) + self.scanno = int(fnowithsuffix.split(".")[0]) except Exception: self.scanno = None logger1.warning("Cannot parse scan number of file %s", filename) - with open(filepath, 'r') as fiof: - + with open(filepath, "r") as fiof: prev = 0 line_counter = 0 - while(True): + while True: line = fiof.readline() - if line.startswith('!'): # skip comments + if line.startswith("!"): # skip comments prev = fiof.tell() line_counter = 0 continue - if line.startswith('%c'): # comment section + if line.startswith("%c"): # comment section line_counter = 0 - self.commentsection = '' + self.commentsection = "" line = fiof.readline() - while(not line.startswith('%') - and not line.startswith('!')): + while not line.startswith("%") and not line.startswith("!"): self.commentsection += line prev = fiof.tell() line = fiof.readline() - if line.startswith('%p'): # parameter section + if line.startswith("%p"): # parameter section line_counter = 0 - self.parameterssection = '' + self.parameterssection = "" line = fiof.readline() - while(not line.startswith('%') - and not line.startswith('!')): + while not line.startswith("%") and not line.startswith("!"): self.parameterssection += line prev = fiof.tell() line = fiof.readline() - if line.startswith('%d'): # data type definitions + if line.startswith("%d"): # data type definitions line_counter = 0 self.datacols = [] self.names = [] self.dtypes = [] line = fiof.readline() - while(line.startswith(' Col')): + while line.startswith(" Col"): splitline = line.split() name = splitline[-2] self.names.append(name) @@ -255,13 +252,16 @@ class FioFile(object): line_counter += 1 if line_counter > ABORTLINENO: - raise IOError("Invalid fio file: Found no data " - "after %s lines" % ABORTLINENO) + raise IOError( + "Invalid fio file: Found no data " + "after %s lines" % ABORTLINENO + ) - self.data = numpy.loadtxt(fiof, - dtype={'names': tuple(self.names), - 'formats': tuple(self.dtypes)}, - comments="!") + self.data = numpy.loadtxt( + fiof, + dtype={"names": tuple(self.names), "formats": tuple(self.dtypes)}, + comments="!", + ) # ToDo: read only last line of file, # which sometimes contains the end of acquisition timestamp. @@ -271,7 +271,7 @@ class FioFile(object): # parse parameter section: try: for line in self.parameterssection.splitlines(): - param, value = line.split(' = ') + param, value = line.split(" = ") self.parameter[param] = value except Exception: logger1.warning("Cannot parse parameter section") @@ -288,7 +288,7 @@ class FioFile(object): raise Exception("acquisition str not found") self.user = l2[:acqpos][4:].strip() - self.start_time = l2[acqpos+len(acquiMarker):].strip() + self.start_time = l2[acqpos + len(acquiMarker) :].strip() commentlines = commentlines[2:] self.comments = "\n".join(commentlines[2:]) @@ -324,15 +324,13 @@ class FioH5NodeDataset(commonh5.Dataset): data_kind = array.dtype.kind if data_kind in ["S", "U"]: - value = numpy.asarray(array, - dtype=text_dtype) + value = numpy.asarray(array, dtype=text_dtype) else: value = array # numerical data is already the correct datatype commonh5.Dataset.__init__(self, name, value, parent, attrs) def __getattr__(self, item): - """Proxy to underlying numpy array methods. - """ + """Proxy to underlying numpy array methods.""" if hasattr(self[()], item): return getattr(self[()], item) @@ -363,11 +361,12 @@ class FioH5(commonh5.File): except Exception as e: raise IOError("FIO file %s cannot be read.") from e - attrs = {"NX_class": to_h5py_utf8("NXroot"), - "file_time": to_h5py_utf8( - datetime.datetime.now().isoformat()), - "file_name": to_h5py_utf8(filename), - "creator": to_h5py_utf8("silx fioh5 %s" % silx_version)} + attrs = { + "NX_class": to_h5py_utf8("NXroot"), + "file_time": to_h5py_utf8(datetime.datetime.now().isoformat()), + "file_name": to_h5py_utf8(filename), + "creator": to_h5py_utf8("silx fioh5 %s" % silx_version), + } commonh5.File.__init__(self, filename, attrs=attrs) if fiof.scanno is not None: @@ -387,33 +386,40 @@ class FioScanGroup(commonh5.Group): :param str scan_key: Scan key (e.g. "1.1") :param scan: FioFile object """ - if hasattr(scan, 'user'): + if hasattr(scan, "user"): userattr = to_h5py_utf8(scan.user) else: - userattr = to_h5py_utf8('') - commonh5.Group.__init__(self, scan_key, parent=parent, - attrs={"NX_class": to_h5py_utf8("NXentry"), - "user": userattr}) + userattr = to_h5py_utf8("") + commonh5.Group.__init__( + self, + scan_key, + parent=parent, + attrs={"NX_class": to_h5py_utf8("NXentry"), "user": userattr}, + ) # 'title', 'start_time' and 'user' are defaults # in Sardana created files: - if hasattr(scan, 'title'): + if hasattr(scan, "title"): title = scan.title else: title = scan_key # use scan number as default title - self.add_node(FioH5NodeDataset(name="title", - data=to_h5py_utf8(title), - parent=self)) + self.add_node( + FioH5NodeDataset(name="title", data=to_h5py_utf8(title), parent=self) + ) - if hasattr(scan, 'start_time'): + if hasattr(scan, "start_time"): start_time = scan.start_time - self.add_node(FioH5NodeDataset(name="start_time", - data=to_h5py_utf8(start_time), - parent=self)) - - self.add_node(FioH5NodeDataset(name="comments", - data=to_h5py_utf8(scan.comments), - parent=self)) + self.add_node( + FioH5NodeDataset( + name="start_time", data=to_h5py_utf8(start_time), parent=self + ) + ) + + self.add_node( + FioH5NodeDataset( + name="comments", data=to_h5py_utf8(scan.comments), parent=self + ) + ) self.add_node(FioInstrumentGroup(parent=self, scan=scan)) self.add_node(FioMeasurementGroup(parent=self, scan=scan)) @@ -426,14 +432,18 @@ class FioMeasurementGroup(commonh5.Group): :param parent: parent Group :param scan: FioFile object """ - commonh5.Group.__init__(self, name="measurement", parent=parent, - attrs={"NX_class": to_h5py_utf8("NXcollection")}) + commonh5.Group.__init__( + self, + name="measurement", + parent=parent, + attrs={"NX_class": to_h5py_utf8("NXcollection")}, + ) for label in scan.names: safe_label = label.replace("/", "%") - self.add_node(FioH5NodeDataset(name=safe_label, - data=scan.data[label], - parent=self)) + self.add_node( + FioH5NodeDataset(name=safe_label, data=scan.data[label], parent=self) + ) class FioInstrumentGroup(commonh5.Group): @@ -443,14 +453,20 @@ class FioInstrumentGroup(commonh5.Group): :param parent: parent Group :param scan: FioFile object """ - commonh5.Group.__init__(self, name="instrument", parent=parent, - attrs={"NX_class": to_h5py_utf8("NXinstrument")}) + commonh5.Group.__init__( + self, + name="instrument", + parent=parent, + attrs={"NX_class": to_h5py_utf8("NXinstrument")}, + ) self.add_node(FioParameterGroup(parent=self, scan=scan)) self.add_node(FioFileGroup(parent=self, scan=scan)) - self.add_node(FioH5NodeDataset(name="comment", - data=to_h5py_utf8(scan.comments), - parent=self)) + self.add_node( + FioH5NodeDataset( + name="comment", data=to_h5py_utf8(scan.comments), parent=self + ) + ) class FioFileGroup(commonh5.Group): @@ -460,16 +476,24 @@ class FioFileGroup(commonh5.Group): :param parent: parent Group :param scan: FioFile object """ - commonh5.Group.__init__(self, name="fiofile", parent=parent, - attrs={"NX_class": to_h5py_utf8("NXcollection")}) - - self.add_node(FioH5NodeDataset(name="comments", - data=to_h5py_utf8(scan.commentsection), - parent=self)) - - self.add_node(FioH5NodeDataset(name="parameter", - data=to_h5py_utf8(scan.parameterssection), - parent=self)) + commonh5.Group.__init__( + self, + name="fiofile", + parent=parent, + attrs={"NX_class": to_h5py_utf8("NXcollection")}, + ) + + self.add_node( + FioH5NodeDataset( + name="comments", data=to_h5py_utf8(scan.commentsection), parent=self + ) + ) + + self.add_node( + FioH5NodeDataset( + name="parameter", data=to_h5py_utf8(scan.parameterssection), parent=self + ) + ) class FioParameterGroup(commonh5.Group): @@ -479,11 +503,19 @@ class FioParameterGroup(commonh5.Group): :param parent: parent Group :param scan: FioFile object """ - commonh5.Group.__init__(self, name="parameter", parent=parent, - attrs={"NX_class": to_h5py_utf8("NXcollection")}) + commonh5.Group.__init__( + self, + name="parameter", + parent=parent, + attrs={"NX_class": to_h5py_utf8("NXcollection")}, + ) for label in scan.parameter: safe_label = label.replace("/", "%") - self.add_node(FioH5NodeDataset(name=safe_label, - data=to_h5py_utf8(scan.parameter[label]), - parent=self)) + self.add_node( + FioH5NodeDataset( + name=safe_label, + data=to_h5py_utf8(scan.parameter[label]), + parent=self, + ) + ) |