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content_reader.py
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content_reader.py
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# -*- coding: utf-8 -*-
"""
Created on 29-08-2022
@author: Gambino R.
"""
from datetime import datetime
import os
from glob import glob
import tkinter as tk
from tkinter.messagebox import NO
import ttkbootstrap as ttk
# from tkinter.filedialog import askdirectory
from read_visupars import read_visupars_parameters
from read_method import read_method_parameters
import pandas as pd
from dateutil.parser import parse
import pydicom
from cest_dict import codify_cest_dict
from pydicom import datadict
class FolderDetails():
def __init__(self, main_dir):
self.main_dir = main_dir
# Initialize data dictionary
self.data = {}
def read_folder_details_raw_images(self):
# Get the list of subfolders into main_dir
self.list_of_dirs = os.listdir(self.main_dir)
# Filter subfolder according by the presence of 2dseq file
self.list_of_dirs = [x for x in self.list_of_dirs if glob(os.path.join(self.main_dir, x).replace("\\", "/") + '/**/2dseq', recursive=True) != []]
# Sort subfolders according to folder name
self.list_of_dirs.sort(key=float)
for i, dir in enumerate(self.list_of_dirs):
# Initialize dictionary key
self.data[str(dir)] = {}
self.data[str(dir)]["FolderName"] = str(dir)
acqp_file = os.path.join(self.main_dir, dir, "acqp")
with open(acqp_file, 'r'):
acqp_content = read_visupars_parameters(acqp_file)
self.data[str(dir)]["ProtocolName"] = acqp_content["ACQ_protocol_name"]
self.data[str(dir)]["Method"] = acqp_content["ACQ_method"]
self.data[str(dir)]["NSlices"] = acqp_content["NSLICES"]
self.data[str(dir)]["SliceThickness[mm]"] = acqp_content["ACQ_slice_thick"]
visu_file = os.path.join(self.main_dir, dir, "visu_pars")
if not os.path.exists(visu_file):
visu_file = glob(os.path.join(self.main_dir, dir).replace("\\", "/") + '/**/visu_pars', recursive=True)[0]
with open(visu_file, 'r'):
visu_content = read_visupars_parameters(visu_file)
if "VisuAcqSize" in visu_content.keys():
if isinstance(visu_content["VisuAcqSize"], (int, float)) == False:
self.data[str(dir)]["MatrixSize"] = str(int(visu_content["VisuAcqSize"][0])) + "x" + str(int(visu_content["VisuAcqSize"][1]))
else:
self.data[str(dir)]["MatrixSize"] = int(visu_content["VisuAcqSize"])
else:
self.data[str(dir)]["MatrixSize"] = None
if "VisuInstanceModality" in visu_content.keys():
self.data[str(dir)]["InstanceModality"] = visu_content["VisuInstanceModality"]
else:
self.data[str(dir)]["InstanceModality"] = ""
if "VisuAcqDate" in visu_content.keys():
if isinstance(visu_content["VisuAcqDate"], str):
dt = parse(visu_content["VisuAcqDate"].replace("<", "").replace(">", ""))
self.data[str(dir)]["AcquisitionDate"] = "/".join([str(dt.date()), str(dt.time())])
else:
dt = visu_content["VisuAcqDate"]
self.data[str(dir)]["AcquisitionDate"] = "/".join([str(dt.date()), str(dt.time())])
method_file = os.path.join(self.main_dir, dir, "method")
with open(method_file, 'r'):
method_content = read_method_parameters(method_file)
if "PVM_SatTransPulse" in method_content.keys():
self.data[str(dir)]["PulseLength[ms]"] = round(float(method_content.get("PVM_SatTransPulse")[0]), 2)
else:
self.data[str(dir)]["PulseLength[ms]"] = ""
if "PVM_SatTransPulseAmpl_uT" in method_content.keys():
self.data[str(dir)]["PulseAmplitude[uT]"] = round(float(method_content.get("PVM_SatTransPulseAmpl_uT")), 2)
else:
self.data[str(dir)]["PulseAmplitude[uT]"] = ""
if "PVM_SatTransPulseLength2" in method_content.keys():
self.data[str(dir)]["PulseLength2[ms]"] = round(float(method_content.get("PVM_SatTransPulseLength2"))/1000, 2)
else:
self.data[str(dir)]["PulseLength2[ms]"] = ""
if "PVM_NSatFreq" in method_content.keys():
self.data[str(dir)]["NSaturationFrequencies"] = int(method_content.get("PVM_NSatFreq"))
else:
self.data[str(dir)]["NSaturationFrequencies"] = ""
# Transform dictionary into Dataframe
self.pd_data = pd.DataFrame.from_dict(self.data, orient="index")
# Sort dataframe according to folder name
self.pd_data.sort_values("FolderName")
def read_folder_details_dcm_images(self):
# Get the list of subfolders into main_dir
self.list_of_dirs = os.listdir(os.path.join(self.main_dir, "MR").replace("\\", "/"))
# Filter subfolder according by the presence of 2dseq file
self.list_of_dirs = [x for x in self.list_of_dirs if glob(os.path.join(self.main_dir, "MR", x).replace("\\", "/") + '/*.dcm', recursive=False) != []]
# Sort subfolders according to folder name
self.list_of_dirs.sort(key=float)
for i, dir in enumerate(self.list_of_dirs):
# Initialize dictionary key
self.data[str(dir)] = {}
self.data[str(dir)]["FolderName"] = str(dir)
current_dir = os.path.join(self.main_dir, "MR", dir)
dcm_file = glob(current_dir + "/*.dcm", recursive=False)[0]
dataset = pydicom.dcmread(dcm_file)
codify_cest_dict(dataset[0x10610010].value)
self.data[str(dir)]["ProtocolName"] = dataset.ProtocolName
self.data[str(dir)]["Method"] = dataset.SequenceName.replace(" ", "")
self.data[str(dir)]["NSlices"] = dataset.NumberOfSlices
self.data[str(dir)]["SliceThickness[mm]"] = dataset.SliceThickness
# self.data[str(dir)]["MatrixSize"] = str(int(dataset.AcquisitionMatrix[1])) + "x" + str(int(dataset.AcquisitionMatrix[2]))
self.data[str(dir)]["MatrixSize"] = list(dataset.AcquisitionMatrix)
self.data[str(dir)]["InstanceModality"] = dataset.Modality
self.data[str(dir)]["AcquisitionDate"] = datetime.strftime(datetime.strptime(dataset.AcquisitionDate, "%Y%m%d"), "%d/%m/%Y")
if "Pulse Length" in dataset[0x10611005].name:
self.data[str(dir)]["PulseLength[ms]"] = dataset[0x10611005].value
if "B1 Saturation" in dataset[0x10611004].name:
self.data[str(dir)]["PulseAmplitude[uT]"] = dataset[0x10611004].value
if "Pulse Length 2" in dataset[0x10611010].name:
self.data[str(dir)]["PulseLength2[ms]"] = dataset[0x10611010].value
if "Measurement Number" in dataset[0x10611013].name:
self.data[str(dir)]["NSaturationFrequencies"] = dataset[0x10611013].value
# Transform dictionary into Dataframe
self.pd_data = pd.DataFrame.from_dict(self.data, orient="index")
# Sort dataframe according to folder name
self.pd_data.sort_values("FolderName")
def save_folder_details(self):
# Save details into the main folder
with open(self.main_dir + "/Content.txt", "w+") as out_file:
string_pd_data = self.pd_data.to_string(header=True, index=False, justify='center')
out_file.write(string_pd_data)
def show_folder_details(self, root):
self.popup = tk.Toplevel(root)
self.popup.geometry("+%d+%d" % (300, 400))
widths = [100, 200, 100, 100, 120, 100, 120, 180, 120, 120, 120, 100]
tree = ttk.Treeview(self.popup)
scrollbar = ttk.Scrollbar(self.popup, orient='vertical', command=tree.yview)
tree.configure(yscrollcommand=scrollbar.set)
columns = [x for x in self.pd_data.columns]
tree['columns'] = [x for x in self.pd_data.columns]
tree.column("#0", width=0, stretch=NO)
tree.heading("#0", text="", anchor=tk.CENTER)
for k, col in enumerate(columns):
tree.column(col, anchor=tk.CENTER, width=widths[k])
tree.heading(col, text=col, anchor=tk.CENTER)
for i in range(self.pd_data.shape[0]):
tree.insert(parent='', index='end', iid=i, text='',
values=list(self.pd_data.values[i]))
tree.pack(side='left')
scrollbar.pack(side='right', fill='y')
# close_btn = ttk.Button(self.popup, text='Close', command=self.popup.destroy)
# close_btn.pack(pady=10)
# if __name__ == "__main__":
# root = tk.Tk()
# # Define the main directory
# main_dir = askdirectory(parent=root, title="Select experiment directory")
# data, dir = read_folder_details(main_dir)
# save_folder_details(data, dir)
# show_folder_details(root, data)
# root.mainloop()