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* update readme * version update * no default config generation * add some checks to config reader * add log * update tests * . * update * add test * change format of vectors in config * version update * plot sequence
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,92 @@ | ||
| #!/usr/bin/env python | ||
|
|
||
| import os | ||
| import sys | ||
| import configparser | ||
| import numpy as np | ||
| import matplotlib.pyplot as plt | ||
| from matplotlib.patches import Rectangle | ||
|
|
||
| def read_ini(file_path): | ||
| config = configparser.ConfigParser() | ||
| config.optionxform = str # Preserve case of keys | ||
| try: | ||
| config_parent_dict = {} | ||
| config.read(file_path) | ||
| if config.has_section('GENERAL'): | ||
| if config.has_option('GENERAL', 'PARENT_CONFIG') and config.get('GENERAL', 'PARENT_CONFIG') != '': | ||
| parent_config = config.get('GENERAL', 'PARENT_CONFIG') | ||
| parent_config_path = os.path.join(os.path.dirname(file_path), parent_config) | ||
| config_parent_dict = read_ini(parent_config_path) | ||
|
|
||
| config_dict = {section: dict(config.items(section)) for section in config.sections()} | ||
| config_combined_dict = {} | ||
| all_keys = config_parent_dict.keys() | config_dict.keys() | ||
| for key in all_keys: | ||
| if key not in config_parent_dict: | ||
| config_parent_dict[key] = {} | ||
| if key not in config_dict: | ||
| config_dict[key] = {} | ||
| config_combined_dict[key] = {**config_parent_dict[key], **config_dict[key]} | ||
|
|
||
| except Exception as e: | ||
| print(f"Error reading INI file: {e}") | ||
| sys.exit(1) | ||
|
|
||
| return config_combined_dict | ||
|
|
||
| def main(): | ||
| if len(sys.argv) != 2: | ||
| print("Usage: python plot_seq.py <file_path>") | ||
| sys.exit(1) | ||
| file_path = sys.argv[1] | ||
|
|
||
| if os.path.exists(file_path) is False : | ||
| print(f"The file '{file_path}' does not exist.") | ||
| sys.exit(1) | ||
|
|
||
| config = read_ini(file_path) | ||
|
|
||
| TR = np.float64(config['SCAN_PARAMETERS']['TR']) | ||
| TE = np.fromstring(config['SCAN_PARAMETERS']["TE"], sep=' ') | ||
|
|
||
| RF_T = np.fromstring(config['SCAN_PARAMETERS']["RF_T"], sep=' ') | ||
| RF_FA = np.fromstring(config['SCAN_PARAMETERS']["RF_FA"], sep=' ') | ||
| RF_PH = np.fromstring(config['SCAN_PARAMETERS']["RF_PH"], sep=' ') | ||
|
|
||
| GRADIENT_T = np.fromstring(config['SCAN_PARAMETERS']["GRADIENT_T"], sep=' ') | ||
| GRADIENT_X = np.fromstring(config['SCAN_PARAMETERS']["GRADIENT_X"], sep=' ') | ||
| GRADIENT_Y = np.fromstring(config['SCAN_PARAMETERS']["GRADIENT_Y"], sep=' ') | ||
| GRADIENT_Z = np.fromstring(config['SCAN_PARAMETERS']["GRADIENT_Z"], sep=' ') | ||
|
|
||
| fig, (ax1, ax2) = plt.subplots(2, 1, figsize=(12, 6)) | ||
| for t, h in zip(RF_T, RF_FA): | ||
| ax1.annotate('', xy=(t, h), xytext=(t, 0), arrowprops=dict(arrowstyle="->")) | ||
|
|
||
| TE_h = np.max(RF_FA)*0.75 | ||
| for te in TE: | ||
| ax1.add_patch(Rectangle((te - 50, 0), 100, TE_h, color='red')) | ||
|
|
||
| ax1.set_xlim(-TR/10, TR) | ||
| ax1.set_ylim(0, np.max(RF_FA)*1.1) | ||
| ax1.spines['top'].set_visible(False) | ||
| ax1.spines['right'].set_visible(False) | ||
| ax1.set_ylabel('Flip Angle (deg)') | ||
|
|
||
| ax2.plot(GRADIENT_T, GRADIENT_X, label='Gradient X') | ||
| ax2.plot(GRADIENT_T, GRADIENT_Y, label='Gradient Y') | ||
| ax2.plot(GRADIENT_T, GRADIENT_Z, label='Gradient Z') | ||
| max_grad = np.max([np.max(GRADIENT_X), np.max(GRADIENT_Y), np.max(GRADIENT_Z)]) | ||
| min_grad = np.min([np.min(GRADIENT_X), np.min(GRADIENT_Y), np.min(GRADIENT_Z)]) | ||
| ax2.set_xlim(-TR/10, TR) | ||
| ax2.set_ylim(min_grad*1.1, max_grad*1.1) | ||
| ax2.spines['top'].set_visible(False) | ||
| ax2.spines['right'].set_visible(False) | ||
| ax2.legend() | ||
| ax2.set_xlabel('Time (ms)') | ||
| ax2.set_ylabel('Gradient Amplitude (mT/m)') | ||
|
|
||
| plt.show() | ||
|
|
||
| if __name__ == "__main__": | ||
| main() |
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