diff --git a/qim3d/io/load.py b/qim3d/io/load.py
index 3df15287e88588928041e401595a05a04579c7ef..2a48536aabb8ddba00560389695d42391d448bae 100644
--- a/qim3d/io/load.py
+++ b/qim3d/io/load.py
@@ -12,16 +12,16 @@ Example:
import difflib
import os
+import re
+import struct
from pathlib import Path
+import dask.array as da
import h5py
import nibabel as nib
import numpy as np
import olefile
-import struct
-import re
-import dask.array as da
-from pathlib import Path
+import pydicom
import tifffile
from PIL import Image, UnidentifiedImageError
@@ -30,6 +30,7 @@ from qim3d.io.logger import log
from qim3d.utils.internal_tools import sizeof, stringify_path
from qim3d.utils.system import Memory
+
class DataLoader:
"""Utility class for loading data from different file formats.
@@ -437,6 +438,39 @@ class DataLoader:
return vol, meta_data
else:
return vol
+
+ def load_dicom(self, path):
+ """ Load a DICOM file
+
+ Args:
+ path (str): Path to file
+ """
+ dcm_data = pydicom.dcmread(path)
+
+ if self.return_metadata:
+ return dcm_data.pixel_array, dcm_data
+ else:
+ return dcm_data.pixel_array
+
+ def load_dicom_dir(self, path):
+ """ Load a directory of DICOM files into a numpy 3d array
+
+ Args:
+ path (str): Directory path
+ """
+ # loop over all .dcm files in the directory
+ files = [f for f in os.listdir(path) if f.endswith('.dcm')]
+ files.sort()
+ # dicom_list contains the dicom objects with metadata
+ dicom_list = [pydicom.dcmread(os.path.join(path, f)) for f in files]
+ # vol contains the pixel data
+ vol = np.stack([dicom.pixel_array for dicom in dicom_list], axis=0)
+
+ if self.return_metadata:
+ return vol, dicom_list
+ else:
+ return vol
+
def load(self, path):
"""
@@ -474,6 +508,8 @@ class DataLoader:
return self.load_nifti(path)
elif path.endswith((".vol",".vgi")):
return self.load_vol(path)
+ elif path.endswith((".dcm",".DCM")):
+ return self.load_dicom(path)
else:
try:
return self.load_pil(path)
@@ -482,7 +518,11 @@ class DataLoader:
# Load a directory
elif os.path.isdir(path):
- return self.load_tiff_stack(path)
+ # load dicom if directory contains dicom files else load tiff stack as default
+ if any([f.endswith('.dcm') for f in os.listdir(path)]):
+ return self.load_dicom_dir(path)
+ else:
+ return self.load_tiff_stack(path)
# Fails
else:
diff --git a/qim3d/io/save.py b/qim3d/io/save.py
index 04cb72d392ec5ec35a8cfd44fbc40e2285bb2583..64a6a1ca5adfd9efab8b7f8d2cb7ebb4f5b25b0f 100644
--- a/qim3d/io/save.py
+++ b/qim3d/io/save.py
@@ -21,13 +21,17 @@ Example:
```
"""
+import datetime
import os
import h5py
import nibabel as nib
import numpy as np
import PIL
+import pydicom
import tifffile
+from pydicom.dataset import FileDataset, FileMetaDataset
+from pydicom.uid import UID
from qim3d.io.logger import log
from qim3d.utils.internal_tools import sizeof, stringify_path
@@ -179,6 +183,59 @@ class DataSaver:
with h5py.File(path, "w") as f:
f.create_dataset("dataset", data=data, compression="gzip" if self.compression else None)
+ def save_dicom(self, path, data):
+ """ Save data to a DICOM file to the given path.
+
+ Args:
+ path (str): The path to save file to
+ data (numpy.ndarray): The data to be saved
+ """
+ # based on https://pydicom.github.io/pydicom/stable/auto_examples/input_output/plot_write_dicom.html
+
+ # Populate required values for file meta information
+ file_meta = FileMetaDataset()
+ file_meta.MediaStorageSOPClassUID = UID('1.2.840.10008.5.1.4.1.1.2')
+ file_meta.MediaStorageSOPInstanceUID = UID("1.2.3")
+ file_meta.ImplementationClassUID = UID("1.2.3.4")
+
+ # Create the FileDataset instance (initially no data elements, but file_meta
+ # supplied)
+ ds = FileDataset(path, {},
+ file_meta=file_meta, preamble=b"\0" * 128)
+
+ ds.PatientName = "Test^Firstname"
+ ds.PatientID = "123456"
+ ds.StudyInstanceUID = "1.2.3.4.5"
+ ds.SamplesPerPixel = 1
+ ds.PixelRepresentation = 0
+ ds.BitsStored = 16
+ ds.BitsAllocated = 16
+ ds.PhotometricInterpretation = "MONOCHROME2"
+ ds.Rows = data.shape[1]
+ ds.Columns = data.shape[2]
+ ds.NumberOfFrames = data.shape[0]
+ # Set the transfer syntax
+ ds.is_little_endian = True
+ ds.is_implicit_VR = True
+
+ # Set creation date/time
+ dt = datetime.datetime.now()
+ ds.ContentDate = dt.strftime('%Y%m%d')
+ timeStr = dt.strftime('%H%M%S.%f') # long format with micro seconds
+ ds.ContentTime = timeStr
+ # Needs to be here because of bug in pydicom
+ ds.file_meta.TransferSyntaxUID = pydicom.uid.ImplicitVRLittleEndian
+
+ # Reshape the data into a 1D array and convert to uint16
+ data_1d = data.ravel().astype(np.uint16)
+ # Convert the data to bytes
+ data_bytes = data_1d.tobytes()
+ # Add the data to the DICOM file
+ ds.PixelData = data_bytes
+
+ ds.save_as(path)
+
+
def save_PIL(self, path, data):
""" Save data to a PIL file to the given path.
@@ -271,6 +328,8 @@ class DataSaver:
return self.save_h5(path, data)
elif path.endswith((".vol",".vgi")):
return self.save_vol(path, data)
+ elif path.endswith((".dcm",".DCM")):
+ return self.save_dicom(path, data)
elif path.endswith((".jpeg",".jpg", ".png")):
return self.save_PIL(path, data)
else:
diff --git a/requirements.txt b/requirements.txt
index 3338fefbe0a3dbd1e5e042a7dd9c1e706deb16b7..30211e80501de6ae6e74d878cebaf520b2acdd41 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -10,6 +10,7 @@ Pillow>=10.0.1,
plotly>=5.14.1,
scipy>=1.11.2,
seaborn>=0.12.2,
+pydicom>=2.4.4,
setuptools>=68.0.0,
tifffile>=2023.4.12,
torch>=2.0.1,
diff --git a/setup.py b/setup.py
index 92b4f0ec7e13262cfac416ac9720bbff345f24fc..93087983974f465470edc846fa8ba8d84eb1d037 100644
--- a/setup.py
+++ b/setup.py
@@ -42,6 +42,7 @@ setup(
"h5py>=3.9.0",
"localthickness>=0.1.2",
"matplotlib>=3.8.0",
+ "pydicom>=2.4.4",
"monai>=1.2.0",
"numpy>=1.26.0",
"outputformat>=0.1.3",