Merge pull request #22 from schuenke/dev

update write_WASABI and move it to examples

README.md

@@ -64,8 +64,10 @@ These are for example _normalize_ (bool: toggle normalization), _norm_threshold_
 normalization offsets), _offsets_ (list/array: manually defined x-values), _invert_ax_ (bool: toggle invert ax), 
 _plot_mtr_asym_ (bool:toggle plot MTR_asym) and _title_, _x_label_, _y_label_ to control the lables.
 
-The [BMCTool GitHub repository](https://github.com/schuenke/BMCTool) contains some further pre-defined examples in the
-[examples folder](examples).
+The [examples folder](examples) in the [BMCTool GitHub repository](https://github.com/schuenke/BMCTool) contains some 
+further simulation examples as well as an example script to create your own _WASABI.seq_ file. _Please note that this
+file will include an additional normalization offset at -300 ppm. To use this for normalization in the simulation,
+simply add the kewword argument ``normalize=True`` to the simulate function._ 
 
 ## Pulseq-CEST Project
 The BMCTool was developed in parallel to the [pulseq-cest project](https://pulseq-cest.github.io/) that aims to provide

bmctool/library/write_wasabi_seq.py → examples/write_WASABI.py

@@ -10,7 +10,6 @@
      T_rec = 2/12 s (saturated/M0)
 """
 
-import os
 import numpy as np
 from pypulseq.Sequence.sequence import Sequence
 from pypulseq.make_adc import make_adc
@@ -21,13 +20,10 @@
 from pypulseq.opts import Opts
 from bmctool.utils.seq.write import write_seq
 
-# get id of generation file
-seqid = os.path.splitext(os.path.basename(__file__))[0]
-
 # general settings
+seqid = 'WASABI'
 author = 'Patrick Schuenke'
-plot_sequence = False  # plot preparation block?
-convert_to_1_3 = True  # convert seq-file to a pseudo version 1.3 file?
+plot_sequence = True  # plot preparation block?
 
 # sequence definitions (everything in seq_defs will be written to definitions of the .seq-file)
 seq_defs:dict = {}
@@ -66,7 +62,7 @@
 
 # RF pulses
 flip_angle_sat = seq_defs['b1cwpe'] * gamma_hz * 2 * np.pi * seq_defs['tp']
-rf_pulse, _ = make_block_pulse(flip_angle=flip_angle_sat, duration=seq_defs['tp'], system=sys)
+rf_pulse = make_block_pulse(flip_angle=flip_angle_sat, duration=seq_defs['tp'], system=sys)
 
 # ADC events
 pseudo_adc = make_adc(num_samples=1, duration=1e-3)  # (not played out; just used to split measurements)
@@ -105,11 +101,10 @@
 
 write_seq(seq=seq,
           seq_defs=seq_defs,
-          filename=seqid+'_py.seq',
+          filename=seqid+'.seq',
           author=author,
-          use_matlab_names=True,
-          convert_to_1_3=convert_to_1_3)
+          use_matlab_names=True)
 
 # plot the sequence
 if plot_sequence:
-    seq.plot(time_range=[0, seq_defs['trec_m0']+seq_defs['tsat']])  # to plot all offsets, remove time_range argument
+    seq.plot()