"""This module provides plugins for various imaging formats.
Standard plugins provides support for DICOM and Nifti image file formats.
"""
# Copyright (c) 2013-2024 Erling Andersen, Haukeland University Hospital, Bergen, Norway
import os
import sys
import time
import uuid
import numpy as np
from pydicom.uid import UID
(SORT_ON_SLICE,
SORT_ON_TAG) = range(2)
sort_on_set = {SORT_ON_SLICE, SORT_ON_TAG}
INPUT_ORDER_AUTO = 'auto'
INPUT_ORDER_NONE = 'none'
INPUT_ORDER_TIME = 'time'
INPUT_ORDER_TRIGGERTIME = 'triggertime'
INPUT_ORDER_B = 'b'
INPUT_ORDER_BVECTOR = 'bvector'
INPUT_ORDER_RSI = 'rsi'
INPUT_ORDER_FA = 'fa'
INPUT_ORDER_TE = 'te'
INPUT_ORDER_FAULTY = 'faulty'
input_order_set = {INPUT_ORDER_NONE, INPUT_ORDER_TIME, INPUT_ORDER_B, INPUT_ORDER_BVECTOR,
INPUT_ORDER_RSI, INPUT_ORDER_FA, INPUT_ORDER_TRIGGERTIME,
INPUT_ORDER_TE, INPUT_ORDER_FAULTY}
[docs]
class NotImageError(Exception):
pass
[docs]
class EmptyImageError(Exception):
pass
[docs]
class UnknownTag(Exception):
pass
[docs]
class NotTimeOrder(Exception):
pass
[docs]
class CannotSort(Exception):
pass
[docs]
class SOPInstanceUIDNotFound(Exception):
pass
[docs]
class WriteNotImplemented(Exception):
pass
[docs]
def sort_on_to_str(sort_on):
if sort_on == SORT_ON_SLICE:
return "SORT_ON_SLICE"
elif sort_on == SORT_ON_TAG:
return "SORT_ON_TAG"
else:
raise (UnknownTag("Unknown numerical sort_on {:d}.".format(sort_on)))
[docs]
def str_to_sort_on(s):
if s == "slice":
return SORT_ON_SLICE
elif s == "tag":
return SORT_ON_TAG
else:
raise (UnknownTag("Unknown sort_on string {}.".format(s)))
[docs]
def str_to_dtype(s):
if s == "none":
return None
elif s == "uint8":
return np.uint8
elif s == "uint16":
return np.uint16
elif s == "int16":
return np.int16
elif s == "int":
return np.int16
elif s == "float":
return np.float
elif s == "float32":
return np.float32
elif s == "float64":
return np.float64
elif s == "double":
return np.double
else:
raise (ValueError("Output data type {} not implemented.".format(s)))
[docs]
def shape_to_str(shape):
"""Convert numpy image shape to printable string
Args:
shape
Returns:
printable shape (str)
Raises:
ValueError: when shape cannot be converted to printable string
"""
if len(shape) == 5:
return "{}x{}tx{}x{}x{}".format(shape[0], shape[1], shape[2], shape[3], shape[4])
elif len(shape) == 4:
return "{}tx{}x{}x{}".format(shape[0], shape[1], shape[2], shape[3])
elif len(shape) == 3:
return "{}x{}x{}".format(shape[0], shape[1], shape[2])
elif len(shape) == 2:
return "{}x{}".format(shape[0], shape[1])
elif len(shape) == 1:
return "{}".format(shape[0])
else:
raise ValueError("Unknown shape")
[docs]
def get_size(obj, seen=None):
"""Recursively finds size of objects"""
size = sys.getsizeof(obj)
if seen is None:
seen = set()
obj_id = id(obj)
if obj_id in seen:
return 0
# Important mark as seen *before* entering recursion to gracefully handle
# self-referential objects
seen.add(obj_id)
if isinstance(obj, dict):
size += sum([get_size(v, seen) for v in obj.values()])
size += sum([get_size(k, seen) for k in obj.keys()])
elif hasattr(obj, '__dict__'):
size += get_size(obj.__dict__, seen)
elif hasattr(obj, '__iter__') and not isinstance(obj, (str, bytes, bytearray)):
size += sum([get_size(i, seen) for i in obj])
return size
[docs]
def get_plugins_list():
from .. import plugins
return plugins['format'] if 'format' in plugins else []
[docs]
def find_plugin(ftype):
"""Return plugin for given format type."""
plugins = get_plugins_list()
for pname, ptype, pclass in plugins:
if ptype == ftype:
return pclass()
raise FormatPluginNotFound("Plugin for format {} not found.".format(ftype))
_my_root = "2.16.578.1.37.1.1.2.{}.{}.{}".format(
hex(uuid.getnode())[2:],
os.getpid(),
int(time.time())
)
[docs]
def get_uid(k=[0]) -> UID:
"""Generator function which will return a unique UID.
"""
while True:
k[0] += 1
yield UID("%s.%d" % (_my_root, k[0]))