DRAFT: Pulseq v1.5.0 implementations

examples/scripts/write_2Dt1_mprage.py

@@ -39,10 +39,11 @@
     apodization=0.5,
     time_bw_product=4,
     return_gz=True,
+    use='excitation',
 )
 
 flip90 = 90 * pi / 180
-rf90 = pp.make_block_pulse(flip_angle=flip90, system=system, duration=500e-6, time_bw_product=4)
+rf90 = pp.make_block_pulse(flip_angle=flip90, system=system, duration=500e-6, time_bw_product=4, use='preparation')
 
 # =========
 # Readout

examples/scripts/write_3Dt1_mprage.py

@@ -28,10 +28,12 @@
 # RF preparatory, excitation
 # =========
 flip_exc = 12 * pi / 180
-rf = pp.make_block_pulse(flip_angle=flip_exc, system=system, duration=250e-6, time_bw_product=4)
+rf = pp.make_block_pulse(flip_angle=flip_exc, system=system, duration=250e-6, time_bw_product=4, use='excitation')
 
 flip_prep = 90 * pi / 180
-rf_prep = pp.make_block_pulse(flip_angle=flip_prep, system=system, duration=500e-6, time_bw_product=4)
+rf_prep = pp.make_block_pulse(
+    flip_angle=flip_prep, system=system, duration=500e-6, time_bw_product=4, use='preparation'
+)
 
 # =========
 # Readout

examples/scripts/write_epi.py

@@ -43,6 +43,7 @@ def main(plot: bool = False, write_seq: bool = False, seq_filename: str = 'epi_p
         time_bw_product=4,
         return_gz=True,
         delay=system.rf_dead_time,
+        use='excitation',
     )
 
     # Define other gradients and ADC events

examples/scripts/write_epi_label.py

@@ -47,6 +47,7 @@ def main(plot: bool = False, write_seq: bool = False, seq_filename: str = 'epi_l
         time_bw_product=4,
         return_gz=True,
         delay=system.rf_dead_time,
+        use='excitation',
     )
 
     # Define trigger

examples/scripts/write_epi_se.py

@@ -39,6 +39,7 @@ def main(plot: bool = False, write_seq: bool = False, seq_filename: str = 'epi_s
         time_bw_product=4,
         return_gz=True,
         delay=system.rf_dead_time,
+        use='excitation',
     )
 
     # Define other gradients and ADC events

examples/scripts/write_epi_se_rs.py

@@ -57,6 +57,7 @@ def main(plot: bool = False, write_seq: bool = False, seq_filename: str = 'epi_s
         bandwidth=np.abs(sat_freq),
         freq_offset=sat_freq,
         delay=system.rf_dead_time,
+        use='saturation',
     )
     gz_fs = pp.make_trapezoid(channel='z', system=system, delay=pp.calc_duration(rf_fs), area=1 / 1e-4)
 
@@ -70,6 +71,7 @@ def main(plot: bool = False, write_seq: bool = False, seq_filename: str = 'epi_s
         time_bw_product=4,
         return_gz=True,
         delay=system.rf_dead_time,
+        use='excitation',
     )
 
     # Create 90 degree slice refocusing pulse and gradients

examples/scripts/write_gre.py

@@ -5,7 +5,7 @@
 import pypulseq as pp
 
 
-def main(plot: bool = False, write_seq: bool = False, seq_filename: str = 'gre_pypulseq.seq'):
+def main(plot: bool = False, write_seq: bool = False, seq_filename: str = 'gre_pypulseq.seq', paper_plot: bool = False):
     # ======
     # SETUP
     # ======
@@ -44,6 +44,7 @@ def main(plot: bool = False, write_seq: bool = False, seq_filename: str = 'gre_p
         system=system,
         return_gz=True,
         delay=system.rf_dead_time,
+        use='excitation',
     )
     # Define other gradients and ADC events
     delta_k = 1 / fov
@@ -120,7 +121,10 @@ def main(plot: bool = False, write_seq: bool = False, seq_filename: str = 'gre_p
     # VISUALIZATION
     # ======
     if plot:
-        seq.plot()
+        if paper_plot:
+            seq.paper_plot()
+        else:
+            seq.plot()
 
     seq.calculate_kspace()
 
@@ -143,4 +147,4 @@ def main(plot: bool = False, write_seq: bool = False, seq_filename: str = 'gre_p
 
 
 if __name__ == '__main__':
-    main(plot=False, write_seq=True)
+    seq = main(plot=True, paper_plot=True, write_seq=False)

examples/scripts/write_gre_label.py

@@ -47,6 +47,7 @@ def main(plot: bool = False, write_seq: bool = False, seq_filename: str = 'gre_l
         system=system,
         return_gz=True,
         delay=system.rf_dead_time,
+        use='excitation',
     )
 
     # Define other gradients and ADC events

examples/scripts/write_haste.py

@@ -72,6 +72,7 @@ def main(plot: bool = False, write_seq: bool = False, seq_filename: str = 'haste
         phase_offset=rfex_phase,
         return_gz=True,
         delay=system.rf_dead_time,
+        use='excitation',
     )
     GS_ex = make_trapezoid(
         channel='z',

examples/scripts/write_mprage.py

@@ -45,9 +45,16 @@ def main(plot: bool = False, write_seq: bool = False, seq_filename: str = 'mprag
     ax.n3 = xyz.index(ax.d3)
 
     # Create alpha-degree hard pulse and gradient
-    rf = pp.make_block_pulse(flip_angle=alpha * np.pi / 180, system=system, duration=rf_len, delay=system.rf_dead_time)
+    rf = pp.make_block_pulse(
+        flip_angle=alpha * np.pi / 180, system=system, duration=rf_len, delay=system.rf_dead_time, use='excitation'
+    )
     rf180 = pp.make_adiabatic_pulse(
-        pulse_type='hypsec', system=system, duration=10.24e-3, dwell=1e-5, delay=system.rf_dead_time
+        pulse_type='hypsec',
+        system=system,
+        duration=10.24e-3,
+        dwell=1e-5,
+        delay=system.rf_dead_time,
+        use='inversion',
     )
 
     # Define other gradients and ADC events

examples/scripts/write_radial_gre.py

@@ -45,6 +45,7 @@ def main(plot: bool = False, write_seq: bool = False, seq_filename: str = 'gre_r
         time_bw_product=4,
         return_gz=True,
         delay=system.rf_dead_time,
+        use='excitation',
     )
 
     # Define other gradients and ADC events

examples/scripts/write_tse.py

@@ -63,6 +63,7 @@ def main(plot: bool = False, write_seq: bool = False, seq_filename: str = 'tse_p
         phase_offset=rf_ex_phase,
         return_gz=True,
         delay=system.rf_dead_time,
+        use='excitation',
     )
     gs_ex = pp.make_trapezoid(
         channel='z',

examples/scripts/write_ute.py

@@ -54,6 +54,7 @@ def main(plot: bool = False, write_seq: bool = False, seq_filename: str = 'ute_p
         system=system,
         return_gz=True,
         delay=system.rf_dead_time,
+        use='excitation',
     )
 
     # Align RO asymmetry to ADC samples

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pypulseq"
-version = "1.4.2.post1"
+version = "1.5.0"
 authors = [{ name = "Keerthi Sravan Ravi", email = "ks3621@columbia.edu" }]
 maintainers = [
   { name = "Bilal Tasdelen" },
@@ -28,6 +28,7 @@ dependencies = [
 
 [project.optional-dependencies]
 sigpy = ["sigpy>=0.1.26"]
+mplcursors = ["mplcursors"]
 test = [
   "coverage",
   "codecov",