add plot sequence (#23)

* 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

Author: aghaeifar

config/config_default.ini

@@ -34,38 +34,24 @@ T2[1] = 41
 ; repetition time in microsecond (integer)
 TR = 10e3
 ; echo time in microsecond (integer)
-TE[0] = 5e3
-TE[1] = 6e3
-TE[2] = 7e3
+TE = 5e3 6e3 7e3
 ; RF Flip angle in degree (float)
-RF_FA[0] = 15.0
-RF_FA[1] = 0.0
-RF_FA[2] = 0.0
+RF_FA = 15.0 0.0 0.0
 ; RF Phase in degree (float). Note PHASE_CYCLING will be added to the phase of the first RF
-RF_PH[0] = 0.0
-RF_PH[1] = 0.0
-RF_PH[2] = 0.0
+RF_PH = 0.0 0.0 0.0
 ; Time to apply RF in microsecond (integer). The first RF start time is always 0.0
-RF_T[0] = 0
-RF_T[1] = 100e3
-RF_T[2] = 200e3
+RF_T = 0 100e3 200e3
 ; Dephasing in degree (float). The initial spin in the population will experience a dephasing of 0.0 degrees. Dephasing will then progressively increase in a linear manner up to the final spin, which will undergo dephasing as specified by the given parameter
-DEPHASING[0] = 
-DEPHASING[1] =
-DEPHASING[2] =
+DEPHASING = 
 ; Time to apply dephasing in microsecond (integer).
-DEPHASING_T[0] = 
-DEPHASING_T[1] =
-DEPHASING_T[2] =
+DEPHASING_T = 
 ; Gradient in mT/m for each axis (float). Each sample is active for one TIME_STEP
 ; GRADIENT_XYZ[x] = 1.0 2.2 1.5
-GRADIENT_XYZ[0] =
-GRADIENT_XYZ[1] = 
-GRADIENT_XYZ[2] = 
+GRADIENT_X =
+GRADIENT_Y = 
+GRADIENT_Z = 
 ; Time to apply gradient in micro-second (integer).
-GRADIENT_T[0] = 
-GRADIENT_T[1] =
-GRADIENT_T[2] = 
+GRADIENT_T = 
 ; time intervals per random-walk in micro-second (integer)
 TIME_STEP  = 50
 ; number of dummy scans to reach steady state. The first RF pulse (RF_FA[0]) is used for excitation in dummy scans. If negative, it will be set to 5T1/TR.

config/gradient.ini

@@ -14,34 +14,21 @@ T2[0] = 1000e3
 
 [SCAN_PARAMETERS]
 TR = 40e3
-TE[0] = 20e3
+TE = 20e3
 
-RF_FA[0] = 90.0
+RF_FA = 90.0
+RF_PH = 90.0
+RF_T = 0
 
-RF_PH[0] = 90.0
+GRADIENT_X = 521.9377 
+GRADIENT_Y = 0.0 
+GRADIENT_Z = 0.0
+GRADIENT_T = 10e3
 
-RF_T[0] = 0
-
-DEPHASING[0] = 
-DEPHASING[1] =
-DEPHASING[2] =
-
-DEPHASING_T[0] = 
-DEPHASING_T[1] =
-DEPHASING_T[2] =
-
-; 
-GRADIENT_XYZ[0] = 521.9377 0.0 0.
-GRADIENT_XYZ[1] = 
-GRADIENT_XYZ[2] = 
-
-GRADIENT_T[0] = 10e3
-GRADIENT_T[1] =
-GRADIENT_T[2] = 
 
 TIME_STEP  = 50
 
 [SIMULATION_PARAMETERS]
 ; use 0 for random seed generation, otherwise use a positive integer to make a reproducible simulation
 NUMBER_OF_SPINS = 1030301
-FOV_SCALE[0] = 1.0
+SCALE[0] = 1.0

config/gre.ini

@@ -4,13 +4,10 @@ SEQ_NAME     = gre
 
 [SCAN_PARAMETERS]
 TR = 40000
-TE[0] = 20000
-
-RF_FA[0] = 90.0
-
-RF_PH[0] = 0.0
-
-RF_T[0] = 0
+TE = 20000
+RF_FA = 90.0
+RF_PH = 0.0
+RF_T = 0
 
 [SIMULATION_PARAMETERS]
 ; use 0 for random seed generation, otherwise use a positive integer to make a reproducible simulation

config/se.ini

@@ -4,16 +4,11 @@ SEQ_NAME    = se
 
 [SCAN_PARAMETERS]
 TR = 40000
-TE[0] = 20000
+TE = 20000
 
-RF_FA[0] = 90.0
-RF_FA[1] = 180.0
-
-RF_PH[0] = 0.0
-RF_PH[1] = 90.0
-
-RF_T[0] = 0
-RF_T[1] = 10000
+RF_FA = 90.0 180.0
+RF_PH = 0.0 90
+RF_T = 0 10000
 
 [SIMULATION_PARAMETERS]
 ; use 0 for random seed generation, otherwise use a positive integer to make a reproducible simulation

config/ssfp.ini

@@ -4,13 +4,10 @@ SEQ_NAME     = ssfp
 
 [SCAN_PARAMETERS]
 TR = 10000
-TE[0] = 5000
-
-RF_FA[0] = 16.0
-
-RF_PH[0] = 0.0
-
-RF_T[0] = 0
+TE = 5000
+RF_FA = 16.0
+RF_PH = 0.0
+RF_T = 0
 
 DUMMY_SCAN  = -1
 PHASE_CYCLING = 180

config/stimulated_echo.ini

@@ -5,30 +5,14 @@ SEQ_NAME    = ste
 
 [SCAN_PARAMETERS]
 TR = 120e3
-TE[0] = 40e3
-TE[1] = 80e3
-
-RF_FA[0] = 90.0
-RF_FA[1] = 90.0
-RF_FA[2] = 90.0
-
-RF_PH[0] = 0.0
-RF_PH[1] = 90.0
-RF_PH[2] = 90.0
-
-RF_T[0] = 0
-RF_T[1] = 20e3
-RF_T[2] = 60e3
-
-DEPHASING[0] = 360
-DEPHASING[1] = 360
-DEPHASING[2] = 720
-DEPHASING[3] = 360
-
-DEPHASING_T[0] = 10e3
-DEPHASING_T[1] = 30e3
-DEPHASING_T[2] = 50e3
-DEPHASING_T[3] = 70e3
+TE = 40e3 80e3
+
+RF_FA = 90.0 90.0 90.0
+RF_PH = 0.0 90.0 90.0
+RF_T = 0 20e3 60e3
+
+DEPHASING = 360 360 720 360
+DEPHASING_T = 10e3 30e3 50e3 70e3
 
 [SIMULATION_PARAMETERS]
 ; use 0 for random seed generation, otherwise use a positive integer to make a reproducible simulation

others/plot_seq.py

@@ -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()

src/config/config_generator.cpp

@@ -42,22 +42,25 @@ bool config_generator::generate_default_config(uint32_t TE_us, uint32_t timestep
     // repetition time in microsecond (integer)
     ini_parent["SCAN_PARAMETERS"]["TR"] = std::to_string(TE_us + timestep_us);
     // echo time in microsecond (integer)
-    ini_parent["SCAN_PARAMETERS"]["TE[0]"] = std::to_string(TE_us);
+    ini_parent["SCAN_PARAMETERS"]["TE"] = std::to_string(TE_us);
     // RF Flip angle in degree (float)
-    ini_parent["SCAN_PARAMETERS"]["RF_FA[0]"] = "90.0";
+    ini_parent["SCAN_PARAMETERS"]["RF_FA"] = "90.0";
     // RF Phase in degree (float). Note PHASE_CYCLING will be added to the phase of the first RF
-    ini_parent["SCAN_PARAMETERS"]["RF_PH[0]"] = "0.0";
+    ini_parent["SCAN_PARAMETERS"]["RF_PH"] = "0.0";
     // Time to apply RF in microsecond (integer). The first RF start time is always 0.0
-    ini_parent["SCAN_PARAMETERS"]["RF_T[0]"] = "0";
+    ini_parent["SCAN_PARAMETERS"]["RF_T"] = "0";
 
     // Dephasing in degree (float). The initial spin in the population will experience a dephasing of 0.0 degrees. Dephasing will then progressively increase in a linear manner up to the final spin, which will undergo dephasing as specified by the given parameter
-    ini_parent["SCAN_PARAMETERS"]["DEPHASING[0]"] = "";
+    ini_parent["SCAN_PARAMETERS"]["DEPHASING"] = "";
     // Time to apply dephasing in microsecond (integer).
-    ini_parent["SCAN_PARAMETERS"]["DEPHASING_T[0]"] = "";
+    ini_parent["SCAN_PARAMETERS"]["DEPHASING_T"] = "";
     // Gradient in mT/m for each axis (float). Each sample is active for one TIME_STEP
-    ini_parent["SCAN_PARAMETERS"]["GRADIENT_XYZ[0]"] = "";
+    ini_parent["SCAN_PARAMETERS"]["GRADIENT_X"] = "";
+    ini_parent["SCAN_PARAMETERS"]["GRADIENT_Y"] = "";
+    ini_parent["SCAN_PARAMETERS"]["GRADIENT_Z"] = "";
     // Time to apply gradient in micro-second (integer).
-    ini_parent["SCAN_PARAMETERS"]["GRADIENT_T[0]"] = "";
+    ini_parent["SCAN_PARAMETERS"]["GRADIENT_T"] = "";
+
     // time intervals per random-walk in micro-second (integer)
     ini_parent["SCAN_PARAMETERS"]["TIME_STEP"] = std::to_string(timestep_us);
     // number of dummy scans to reach steady state. The first RF pulse (RF_FA[0]) is used for excitation in dummy scans. If negative, it will be set to 5T1/TR.
@@ -98,10 +101,11 @@ bool config_generator::generate_gre(uint32_t TE_us, uint32_t timestep_us, std::v
         add_param("FILES", "PHANTOM[" + std::to_string(i) + "]", phantoms[i]);
 
     add_param("SCAN_PARAMETERS", "TR", std::to_string(TE_us + timestep_us));
-    add_param("SCAN_PARAMETERS", "TE[0]", std::to_string(TE_us));
-    add_param("SCAN_PARAMETERS", "RF_FA[0]", "90.0");
-    add_param("SCAN_PARAMETERS", "RF_PH[0]", "0");
-    add_param("SCAN_PARAMETERS", "RF_T[0]", "0");
+    add_param("SCAN_PARAMETERS", "TE", std::to_string(TE_us));
+    add_param("SCAN_PARAMETERS", "RF_FA", "90.0");
+    add_param("SCAN_PARAMETERS", "RF_PH", "0");
+    add_param("SCAN_PARAMETERS", "RF_T", "0");
+
     add_param("SCAN_PARAMETERS", "TIME_STEP", std::to_string(timestep_us));
 
     if(output.empty() == false)
@@ -124,19 +128,17 @@ bool config_generator::generate_se(uint32_t TE_us, uint32_t timestep_us, std::ve
         add_param("FILES", "PHANTOM[" + std::to_string(i) + "]", phantoms[i]);
 
     add_param("SCAN_PARAMETERS", "TR", std::to_string(TE_us + timestep_us));
-    add_param("SCAN_PARAMETERS", "TE[0]", std::to_string(TE_us));
-    add_param("SCAN_PARAMETERS", "RF_FA[0]", "90.0");
-    add_param("SCAN_PARAMETERS", "RF_FA[1]", "180.0");
-    add_param("SCAN_PARAMETERS", "RF_PH[0]", "0");
-    add_param("SCAN_PARAMETERS", "RF_PH[1]", "90");
-    add_param("SCAN_PARAMETERS", "RF_T[0]", "0");
-    add_param("SCAN_PARAMETERS", "RF_T[1]", std::to_string(TE_us/2));
+    add_param("SCAN_PARAMETERS", "TE", std::to_string(TE_us));
+    add_param("SCAN_PARAMETERS", "RF_FA", "90.0 180.0");
+    add_param("SCAN_PARAMETERS", "RF_PH", "0 90");
+    add_param("SCAN_PARAMETERS", "RF_T", "0 " + std::to_string(TE_us/2));
     add_param("SCAN_PARAMETERS", "TIME_STEP", std::to_string(timestep_us));
 
     if(output.empty() == false)
         if(write_ini(output) == false)
             return false;
 
+
     return true;
 }
 
@@ -153,10 +155,11 @@ bool config_generator::generate_bssfp(uint32_t TE_us, uint32_t timestep_us, std:
         add_param("FILES", "PHANTOM[" + std::to_string(i) + "]", phantoms[i]);
 
     add_param("SCAN_PARAMETERS", "TR", std::to_string(TE_us*2));
-    add_param("SCAN_PARAMETERS", "TE[0]", std::to_string(TE_us));
-    add_param("SCAN_PARAMETERS", "RF_FA[0]", "16.0");
-    add_param("SCAN_PARAMETERS", "RF_PH[0]", "0");
-    add_param("SCAN_PARAMETERS", "RF_T[0]", "0");
+    add_param("SCAN_PARAMETERS", "TE", std::to_string(TE_us));
+    add_param("SCAN_PARAMETERS", "RF_FA", "16.0");
+    add_param("SCAN_PARAMETERS", "RF_PH", "0");
+    add_param("SCAN_PARAMETERS", "RF_T", "0");
+
     add_param("SCAN_PARAMETERS", "TIME_STEP", std::to_string(timestep_us));
     add_param("SCAN_PARAMETERS", "DUMMY_SCAN", "-1");
     add_param("SCAN_PARAMETERS", "PHASE_CYCLING", "180");

src/definitions.h

@@ -3,7 +3,8 @@
 
 #define VERSION_MAJOR 1
 #define VERSION_MINOR 18
-#define VERSION_PATCH 3
+#define VERSION_PATCH 4
+
 
 // Helper macros to stringify values
 #define STRINGIFY_HELPER(x) #x