1+ import argparse
2+ import os
3+ from pathlib import Path
4+ import subprocess
5+ import sys
6+ import inquirer
7+
8+ def prompt_input_directory ():
9+ return inquirer .prompt ([
10+ inquirer .Path (
11+ "path" ,
12+ message = "📂 Select an input directory containing DICOM image files:" ,
13+ path_type = inquirer .Path .DIRECTORY ,
14+ exists = True ,
15+ )
16+ ])["path" ]
17+
18+
19+ def prompt_output_directory (input_dir ):
20+ # List subfolders of input_dir
21+ subdirs = [
22+ name for name in os .listdir (input_dir )
23+ if os .path .isdir (os .path .join (input_dir , name ))
24+ ]
25+
26+ choices = [f"./{ name } for name in subdirs ]
27+ choices .append ("📥 Enter a custom output path..." )
28+
29+ answer = inquirer .prompt ([
30+ inquirer .List (
31+ "choice" ,
32+ message = f"📁 Choose an output directory for NIfTI files from:\n → { input_dir } ,
33+ choices = choices
34+ )
35+ ])["choice" ]
36+
37+ if answer == "📥 Enter a custom output path..." :
38+ return inquirer .prompt ([
39+ inquirer .Path (
40+ "custom_path" ,
41+ message = "📥 Enter custom output directory path:" ,
42+ path_type = inquirer .Path .DIRECTORY ,
43+ exists = True
44+ )
45+ ])["custom_path" ]
46+ else :
47+ return os .path .abspath (os .path .join (input_dir , answer .strip ("./" )))
48+
49+
50+ def dicom_to_niix (vol_dir : Path , out_dir : Path , merge_2d : bool = False ):
51+ """
52+ For converting DICOM images to a (compresssed) 4d nifti image
53+ """
54+ os .makedirs (out_dir , exist_ok = True )
55+
56+ try :
57+ res = subprocess .run (
58+ [
59+ "dcm2niix" ,
60+ "-f" , "%s_%p" , # dcm2niix attempts to provide a sensible file naming scheme
61+ "-o" , out_dir , # output directory
62+ "-z" , "y" , #specifying compressed nii.gz file
63+ "-m" , "y" if merge_2d else "n" , # Add merge option
64+ # https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage
65+ # for further configuration for general usage see page above
66+ vol_dir # input directory
67+ ],
68+ capture_output = True ,
69+ text = True ,
70+ check = True
71+ )
72+
73+ nifti_files = list (Path (out_dir ).glob ("*.nii.gz" ))
74+ if len (nifti_files ) != 1 :
75+ raise RuntimeError ("Only one NIfTI (.nii.gz) should be in this output directory." )
76+
77+ bval_files = list (out_dir .glob ("*.bval" ))
78+ bvec_files = list (out_dir .glob ("*.bvec" ))
79+ bval_path = str (bval_files [0 ]) if bval_files else None
80+ bvec_path = str (bvec_files [0 ]) if bvec_files else None
81+
82+ if not bval_path or not bvec_path :
83+ raise RuntimeError ("No bvec or bval files were generated." )
84+
85+ return nifti_files [0 ], bval_path , bvec_path
86+
87+ except subprocess .CalledProcessError as e :
88+ raise RuntimeError (f"dcm2niix failed: { e .stderr } )
89+
90+ def run_interactive ():
91+
92+ input_dirs = []
93+ output_dirs = []
94+
95+ while True :
96+ input_dir = prompt_input_directory ()
97+ output_dir = prompt_output_directory (input_dir )
98+
99+ input_dirs .append (input_dir )
100+ output_dirs .append (output_dir )
101+
102+ add_more = inquirer .prompt ([
103+ inquirer .Confirm ("more" , message = "➕ Add another input/output pair?" , default = False )
104+ ])["more" ]
105+
106+ if not add_more :
107+ break
108+
109+ merge_answer = inquirer .prompt ([
110+ inquirer .Confirm ("merge" , message = "🧩 Merge 2D slices into a single NIfTI (-m y)?" , default = True )
111+ ])
112+ merge_2d = merge_answer ["merge" ]
113+
114+ for in_dir , out_dir in zip (input_dirs , output_dirs ):
115+ vol_dir = Path (in_dir )
116+ out_path = Path (out_dir )
117+
118+ print (f"Converting:\n → Input: { vol_dir } \n → Output: { out_path } )
119+ try :
120+ nifti , bval , bvec = dicom_to_niix (vol_dir , out_path , merge_2d )
121+ print (f"✅ Created: { nifti } )
122+ except RuntimeError as err :
123+ print (f"❌ Conversion failed: { err } )
124+
125+ def run_cli (input_path : str , output_path : str ):
126+ vol_dir = Path (input_path )
127+ out_dir = Path (output_path )
128+
129+ print (f" Converting:\n → Input: { vol_dir } \n → Output: { out_dir } )
130+ try :
131+ nifti , bval , bvec = dicom_to_niix (vol_dir , out_dir , merge_2d = False )
132+ print (f" Created NIfTI: { nifti } )
133+
134+ if bval and bvec :
135+ print (" Running IVIM fitting algorithm..." )
136+ subprocess .run ([
137+ "python3" , "-m" , "WrapImage.nifti_wrapper" ,
138+ str (nifti ), str (bvec ), str (bval )
139+ ], check = True )
140+ print (" IVIM fitting complete." )
141+ else :
142+ print ("⚠️ bvec/bval missing, skipping IVIM post-processing." )
143+ except RuntimeError as err :
144+ print (f"❌ Conversion failed: { err } )
145+ sys .exit (1 )
146+
147+ if __name__ == "__main__" :
148+ parser = argparse .ArgumentParser (description = "DICOM to NIfTI converter with optional IVIM processing" )
149+ parser .add_argument ("input" , nargs = "?" , help = "Path to input DICOM directory" )
150+ parser .add_argument ("output" , nargs = "?" , help = "Path to output directory for NIfTI files" )
151+ parser .add_argument ("-pu" , "--prompt-user" , action = "store_true" , help = "Run in interactive mode" )
152+
153+ args = parser .parse_args ()
154+
155+ if args .prompt_user :
156+ run_interactive ()
157+ elif args .input and args .output :
158+ run_cli (args .input , args .output )
159+ else :
160+ print ("❗ You must provide input and output paths OR use --prompt-user for interactive mode." )
161+ parser .print_help ()
162+ sys .exit (1 )
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