jgrewe/nixview-python
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[plot] works for 1 and 2d categories

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This commit is contained in:
Jan Grewe
2021-04-02 20:06:18 +02:00
parent 41ccbfb0a1
commit d77b0b9e9a
3 changed files with 105 additions and 125 deletions
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10
nixview/util/dataview.py
View File

@@ -28,10 +28,10 @@ class DataView():
for i, x in enumerate(zip(self._offset, valid_count)):
if i == self._cut_dim:
new_ofst[i] = sum(x)
self._offset = tuple(new_ofst)
self._fetched_data = tuple([sum(x) for x in zip(self._fetched_data, valid_count)])
def init_chunking(self):
"""decides on the chunks size for reading. Heuristic is based on the dimensionality of the data and the "best xdim" if available.
If data is 2D the best xdim is loaded in chunks (if necessary) while the other is fully loaded. For 3D and more it is the last dimension that is cut. If the number of data points in the first n-1 dimensions exceeds the maximum chunksize (settings) an error will be thrown.
@@ -59,16 +59,15 @@ class DataView():
self._buffer = np.empty(self._full_shape)
except:
raise ValueError("Error reserving buffer! Cannot handle so many data points!") #FIXME
print("init buffer")
@property
def fully_loaded(self):
return np.all(self._buffer is not None and self._fetched_data == self._full_shape)
@property
def full_shape(self):
return self._full_shape
@property
def current_shape(self):
return self._fetched_data
@@ -79,4 +78,3 @@ class DataView():
r += " max chunk size: " + str(self._count)
r += " is fully loaded: " + str(self.fully_loaded)
return r

80
nixview/util/file_handler.py
View File

@@ -8,6 +8,7 @@ from nixview.util.enums import NodeType, PlotterTypes
class Singleton(type):
_instances = {}
def __call__(cls, *args, **kwargs):
if cls not in cls._instances:
cls._instances[cls] = super(Singleton, cls).__call__(*args, **kwargs)
@@ -19,29 +20,29 @@ class EntityBuffer():
def __init__(self) -> None:
super().__init__()
self._buffer = {}
def put(self, entity):
if not hasattr(entity, "id"):
return
id = entity.id
if id not in self._buffer.keys():
self._buffer[id] = entity
def has(self, id):
return id in self._buffer.keys()
def get(self, id):
if self.has(id):
return self._buffer[id]
else:
return None
def clear(self):
self._buffer.clear()
class FileHandler(metaclass=Singleton):
def __init__(self) -> None:
super().__init__()
self._filename = None
@@ -50,24 +51,24 @@ class FileHandler(metaclass=Singleton):
self._entity_buffer = EntityBuffer()
self._file_descriptor = None
self._file_version = None
def open(self, filename):
self.close()
if not os.path.exists(filename):
return False, "File %s could not be found!" % filename
try:
self._nix_file = nix.File.open(filename, nix.FileMode.ReadOnly)
self._filename = filename
self._file_descriptor = FileDescriptor(self.filename, self._nix_file.format, self._nix_file.version,
self._nix_file.created_at, self._nix_file.updated_at, os.path.getsize(self.filename)/1e+6)
self._file_descriptor = FileDescriptor(self.filename, self._nix_file.format, self._nix_file.version,
self._nix_file.created_at, self._nix_file.updated_at, os.path.getsize(self.filename) / 1e+6)
self.file_descriptor.block_count = len(self._nix_file.blocks)
for b in self._nix_file.blocks:
self.file_descriptor.data_array_count += len(b.data_arrays)
self.file_descriptor.group_count += len(b.groups)
self.file_descriptor.tag_count += len(b.tags)
self.file_descriptor.tag_count += len(b.multi_tags)
if hasattr(b, "data_frames"):
if hasattr(b, "data_frames"):
self.file_descriptor.data_frame_count += len(b.data_frames)
self._file_version = self._nix_file.version
return True, "Successfully opened file %s." % filename.split(os.sep)[-1]
@@ -92,11 +93,11 @@ class FileHandler(metaclass=Singleton):
@property
def is_valid(self):
return self._nix_file is not None and self._nix_file.is_open()
@property
def filename(self):
return self._filename
def valid_count(self, shape, offset, count):
valid_count = np.empty(len(shape), dtype=int)
for i, (o, c) in enumerate(zip(offset, count)):
@@ -105,13 +106,13 @@ class FileHandler(metaclass=Singleton):
else:
valid_count[i] = c
return valid_count
def count_is_valid(self, shape, offset, count):
res = True
for s, o, c in zip(shape, offset, count):
res = res and o + c <= s
return res
def request_data(self, entity_descriptor, offset=None, count=None):
entity = self._entity_buffer.get(entity_descriptor.id)
if entity is None:
@@ -131,7 +132,7 @@ class FileHandler(metaclass=Singleton):
else:
item = ItemDescriptor(fs.name, fs.id, fs.type, definition=fs.definition, entity_type=NodeType.Section)
return item
def request_metadata(self, root_id=None, depth=1):
"""[summary]
@@ -145,19 +146,19 @@ class FileHandler(metaclass=Singleton):
self._entity_buffer.put(s)
sub_sections.append(ItemDescriptor(s.name, s.id, s.type, definition=s.definition, entity_type=NodeType.Section))
return sub_sections
def get_properties(section):
props = []
for p in section.props:
value = ""
if self._file_version < (1,1,1):
vals = p.values
if self._file_version < (1, 1, 1):
vals = p.values
if len(vals) > 1:
value += "["
value += ",".join(map(str, [v.value for v in vals]))
value += "]"
else:
value = str(vals[0].value)
value = str(vals[0].value)
else:
vals = p.values
value += "["
@@ -207,7 +208,7 @@ class FileHandler(metaclass=Singleton):
point_or_segment = "segment" if e.extent else "point"
start = str(e.position)
end = ("to " + str(tuple(np.array(e.position) + np.array(e.extent)))) if e.extent else ""
itd.value = "tags %s %s %s" %(point_or_segment, start, end)
itd.value = "tags %s %s %s" % (point_or_segment, start, end)
# TODO set the value to something meaningful for the various entity types
return infos
@@ -219,7 +220,7 @@ class FileHandler(metaclass=Singleton):
if not b:
b = self._nix_file.blocks[id]
return b
def request_data_arrays(self, block_id):
b = self.get_block(block_id)
return self._entity_info(b.data_arrays, block_id, NodeType.DataArray)
@@ -262,10 +263,11 @@ class FileHandler(metaclass=Singleton):
dimensions = []
for i, d in enumerate(da.dimensions):
dim_name = "%i. dim: %s" % (i+1, d.label if hasattr(d, "label") else "")
dim_type= "%s %s" % (d.dimension_type, "dimension")
dim_type = "%s %s" % (d.dimension_type, "dimension")
unit = d.unit if hasattr(d, "unit") else None
label = d.label if hasattr(d, "label") else None
dimensions.append(ItemDescriptor(dim_name, type=dim_type, entity_type=NodeType.Dimension, block_id=block_id, unit=unit, label=label))
dimensions.append(ItemDescriptor(dim_name, type=dim_type, entity_type=NodeType.Dimension,
block_id=block_id, unit=unit, label=label))
return dimensions
def request_axis(self, block_id, array_id, dimension_index, count, start=0):
@@ -273,6 +275,7 @@ class FileHandler(metaclass=Singleton):
if da is None:
b = self.get_block(block_id)
da = b.data_arrays[array_id]
dim = da.dimensions[dimension_index]
if dim.dimension_type == nix.DimensionType.Set:
labels = dim.labels
@@ -280,7 +283,7 @@ class FileHandler(metaclass=Singleton):
raise ValueError("Invalid argument for start or count for SetDimension")
axis = labels[start:start + count]
if len(labels) == 0:
axis = list(map(str, range(start, start+count)))
axis = list(map(str, range(start, start+count)))
else:
axis = np.asarray(dim.axis(count, start))
return axis
@@ -311,7 +314,7 @@ class FileHandler(metaclass=Singleton):
for src in srcs:
sources.extend(get_subsources(src))
return sources
def guess_best_xdim(self, array):
data_extent = array.shape
if len(data_extent) > 2:
@@ -320,23 +323,24 @@ class FileHandler(metaclass=Singleton):
if len(data_extent) == 1:
return 0
d1 = array.dimensions[0]
d2 = array.dimensions[1]
d0 = array.dimensions[0]
d1 = array.dimensions[1]
shape = array.data_extent
if d1.dimension_type == nix.DimensionType.Sample:
if d0.dimension_type == nix.DimensionType.Sample:
return 0
elif d2.dimension_type == nix.DimensionType.Sample:
elif d1.dimension_type == nix.DimensionType.Sample:
return 1
else:
if (d1.dimension_type == nix.DimensionType.Set) and \
(d2.dimension_type == nix.DimensionType.Range):
if (d0.dimension_type == nix.DimensionType.Set) and \
(d1.dimension_type == nix.DimensionType.Range):
return 1
elif (d1.dimension_type == nix.DimensionType.Range) and \
(d2.dimension_type == nix.DimensionType.Set):
return 0
elif (d0.dimension_type == nix.DimensionType.Set) and \
(d1.dimension_type == nix.DimensionType.Set):
return int(np.argmax(shape))
else:
return 0
def suggested_plotter(self, array):
if len(array.dimensions) > 3:
print("cannot handle more than 3D")
@@ -358,19 +362,19 @@ class FileHandler(metaclass=Singleton):
elif dim_count == 2:
if dim_types[0] == nix.DimensionType.Sample:
if dim_types[1] == nix.DimensionType.Sample or \
dim_types[1] == nix.DimensionType.Range:
dim_types[1] == nix.DimensionType.Range:
return PlotterTypes.ImagePlotter
else:
return PlotterTypes.LinePlotter
elif dim_types[0] == nix.DimensionType.Range:
if dim_types[1] == nix.DimensionType.Sample or \
dim_types[1] == nix.DimensionType.Range:
dim_types[1] == nix.DimensionType.Range:
return PlotterTypes.ImagePlotter
else:
return PlotterTypes.LinePlotter
elif dim_types[0] == nix.DimensionType.Set:
if dim_types[1] == nix.DimensionType.Sample or \
dim_types[1] == nix.DimensionType.Range:
dim_types[1] == nix.DimensionType.Range:
return PlotterTypes.LinePlotter
else:
return PlotterTypes.CategoryPlotter