From 8e0a76c4e1fa738e8f63e69f9c5593624ca59ec1 Mon Sep 17 00:00:00 2001
From: Tamino Huxohl <thuxohl@techfak.uni-bielefeld.de>
Date: Thu, 22 Dec 2022 14:47:44 +0100
Subject: [PATCH] refactor interfile module
---
mu_map/file/interfile.py | 108 +++++++++++++++++++++++----------------
1 file changed, 65 insertions(+), 43 deletions(-)
diff --git a/mu_map/file/interfile.py b/mu_map/file/interfile.py
index 85cef0a..a916dda 100644
--- a/mu_map/file/interfile.py
+++ b/mu_map/file/interfile.py
@@ -4,34 +4,6 @@ from typing import Dict, Tuple
import numpy as np
-Interfile = Tuple[Dict[str, str], np.ndarray]
-
-@dataclass
-class _InterfileKeys:
- """
- Data class defining keys for an Interfile header.
- """
- placeholder: str = "{_}"
-
- _dim: str = f"matrix size [{placeholder}]"
- _spacing: str = f"scaling factor (mm/pixel) [{placeholder}]"
-
- data_file: str = "name of data file"
- n_projections: str = "number of projections"
- bytes_per_pixel: str = "number of bytes per pixel"
- number_format: str = "number format"
-
- patient_orientation: str = "patient orientation"
- patient_rotation: str = "supine"
-
- def dim(self, index: int) -> str:
- return self._dim.replace(self.placeholder, str(index))
-
- def spacing(self, index: int) -> str:
- return self._spacing.replace(self.placeholder, str(index))
-
-InterfileKeys = _InterfileKeys()
-
"""
A template of an INTERFILE header.
@@ -70,6 +42,54 @@ END OF INTERFILE :=
"""
+"""
+Default extension for the Interfile header.
+"""
+EXTENSION_INTERFILE_HEADER = ".hv"
+"""
+Default extension for the Interfile image.
+"""
+EXTENSION_INTERFILE_IMAGE = ".v"
+
+
+@dataclass
+class Interfile:
+ """
+ Interfile data type wrapping the header and the image
+ into an object.
+ """
+ header: Dict[str, str]
+ image: np.ndarray
+
+ def __iter__(self):
+ return iter((self.header, self.image))
+
+
+@dataclass
+class _InterfileKeys:
+ """
+ Data class defining keys for an Interfile header.
+ """
+ placeholder: str = "{_}"
+
+ _dim: str = f"matrix size [{placeholder}]"
+ _spacing: str = f"scaling factor (mm/pixel) [{placeholder}]"
+
+ data_file: str = "name of data file"
+ n_projections: str = "number of projections"
+ bytes_per_pixel: str = "number of bytes per pixel"
+ number_format: str = "number format"
+
+ patient_orientation: str = "patient orientation"
+ patient_rotation: str = "supine"
+
+ def dim(self, index: int) -> str:
+ return self._dim.replace(self.placeholder, str(index))
+
+ def spacing(self, index: int) -> str:
+ return self._spacing.replace(self.placeholder, str(index))
+InterfileKeys = _InterfileKeys()
+
def type_by_format(number_format: str, bytes_per_pixel: int) -> type:
"""
@@ -114,7 +134,7 @@ def parse_interfile_header(filename: str) -> Dict[str, str]:
return parse_interfile_header_str(f.read())
-def load_interfile(filename: str) -> Tuple[Dict[str, str], np.ndarray]:
+def load_interfile(filename: str) -> Interfile:
"""
Load an INTERFILE header and its image as a numpy array.
@@ -135,7 +155,7 @@ def load_interfile(filename: str) -> Tuple[Dict[str, str], np.ndarray]:
with open(data_file, mode="rb") as f:
image = np.frombuffer(f.read(), dtype)
image = image.reshape((dim_z, dim_y, dim_x))
- return header, image.copy()
+ return Interfile(header, image.copy())
def load_interfile_img(filename: str) -> np.ndarray:
@@ -145,14 +165,16 @@ def load_interfile_img(filename: str) -> np.ndarray:
:param filename: the filename of the INTERFILE header file
:return: the image as a numpy array
"""
- _, image = load_interfile(filename)
- return image
+ interfile = load_interfile(filename)
+ return interfile.image
-def write_interfile(filename: str, header: Dict[str, str], image: np.ndarray):
+def write_interfile(filename: str, interfile: Interfile):
filename = os.path.splitext(filename)[0]
- filename_data = f"{filename}.v"
- filename_header = f"{filename}.hv"
+ filename_data = f"{filename}{EXTENSION_INTERFILE_IMAGE}"
+ filename_header = f"{filename}{EXTENSION_INTERFILE_HEADER}"
+
+ header, image = interfile
header[InterfileKeys.data_file] = os.path.basename(filename_data)
header[InterfileKeys.dim(3)] = str(image.shape[0])
@@ -181,34 +203,34 @@ if __name__ == "__main__":
args = parser.parse_args()
args.out = args.interfile if args.out is None else args.out
- header, image = load_interfile(args.interfile)
+ interfile = load_interfile(args.interfile)
if args.cmd == "fill":
value = args.param
- image.fill(value)
+ interfile.image.fill(value)
if args.cmd == "pad":
target_size = args.param
- real_size = image.shape[0]
+ real_size = interfile.image.shape[0]
assert target_size > real_size, f"Cannot pad from a larger size {real_size} to a smaller size {target_size}"
diff = target_size - real_size
pad_lower = math.ceil(diff / 2)
pad_upper = math.floor(diff / 2)
- image = np.pad(image, ((pad_lower, pad_upper), (0, 0), (0, 0)))
+ interfile.image = np.pad(interfile.image, ((pad_lower, pad_upper), (0, 0), (0, 0)))
if args.cmd == "crop":
target_size = args.param
- real_size = image.shape[0]
+ real_size = interfile.image.shape[0]
assert target_size < real_size, f"Cannot crop from a smaller size {real_size} to a larger size {target_size}"
diff = target_size / 2
center = real_size // 2
crop_lower = center - math.floor(diff)
crop_upper = center + math.ceil(diff)
- image = image[crop_lower:crop_upper]
+ interfile.image = interfile.image[crop_lower:crop_upper]
if args.cmd == "flip":
- image = image[:, :, ::-1]
+ interfile.image = interfile.image[:, :, ::-1]
- write_interfile(args.out, header, image)
+ write_interfile(args.out, interfile)
--
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