From c72be61c0f0efad40c180e39ef6474424dcda120 Mon Sep 17 00:00:00 2001
From: jupfi <git@jupfi.me>
Date: Tue, 18 Jun 2024 16:19:50 +0200
Subject: [PATCH] Moved example sequences to base repo.

---
 src/quackseq/sequences/COMPFID.py | 30 +++++++++++++++++++++++++++++
 src/quackseq/sequences/FID.py     | 18 +++++++++++++++++
 src/quackseq/sequences/SE.py      | 19 ++++++++++++++++++
 src/quackseq/sequences/SEPC.py    | 32 +++++++++++++++++++++++++++++++
 4 files changed, 99 insertions(+)
 create mode 100644 src/quackseq/sequences/COMPFID.py
 create mode 100644 src/quackseq/sequences/FID.py
 create mode 100644 src/quackseq/sequences/SE.py
 create mode 100644 src/quackseq/sequences/SEPC.py

diff --git a/src/quackseq/sequences/COMPFID.py b/src/quackseq/sequences/COMPFID.py
new file mode 100644
index 0000000..942d2a1
--- /dev/null
+++ b/src/quackseq/sequences/COMPFID.py
@@ -0,0 +1,30 @@
+"""Composite FID example.
+
+This example demonstrates how to simulate a composite FID signal using the quackseq simulator.
+
+See the paper: 
+Sauer, K.L., Klug, C.A., Miller, J.B. et al. Using quaternions to design composite pulses for spin-1 NQR. Appl. Magn. Reson. 25, 485–500 (2004). https://doi.org/10.1007/BF03166543
+
+This also works for Samples with spin > 1.
+"""
+
+from quackseq.pulsesequence import QuackSequence
+from quackseq.functions import RectFunction
+
+def create_COMPFID():
+
+    COMPFID = QuackSequence("COMPFID")
+    COMPFID.add_pulse_event("tx1", "3u", 100, 0, RectFunction())
+    COMPFID.add_pulse_event("tx2", "6u", 100, 45, RectFunction())
+    # This makes the phase 45, 135, 225, 315 (because of the previous 45 degree phase shift and 360/4 = 90 degree phase shift)
+    COMPFID.set_tx_n_phase_cycles("tx2", 4)
+    COMPFID.add_blank_event("blank", "5u")
+    
+    COMPFID.add_readout_event("rx", "100u")
+
+    # No phase shifiting of the receive data but weighting of -1 for the 45 degree pulse, +1 for the 135 degree pulse, -1 for the 225 degree pulse and +1 for the 315 degree pulse
+    readout_scheme = [[1, 0], [-1, 0], [1, 0], [-1, 0]]
+
+    COMPFID.set_rx_readout_scheme("rx", readout_scheme)
+
+    return COMPFID
\ No newline at end of file
diff --git a/src/quackseq/sequences/FID.py b/src/quackseq/sequences/FID.py
new file mode 100644
index 0000000..af501b1
--- /dev/null
+++ b/src/quackseq/sequences/FID.py
@@ -0,0 +1,18 @@
+"""Simple FID sequence with a single excitation pulse and readout event."""
+
+from quackseq.pulsesequence import QuackSequence
+from quackseq.functions import RectFunction
+
+def create_FID() -> QuackSequence:
+    """Creates a simple FID sequence with a single excitation pulse and readout event.
+    
+    Returns:
+        QuackSequence: The FID sequence
+    """
+    FID = QuackSequence("FID")
+    FID.add_pulse_event("tx", "3u", 100, 0, RectFunction())
+    FID.add_blank_event("blank", "5u")
+    FID.add_readout_event("rx", "100u")
+    FID.add_blank_event("TR", "1m")
+
+    return FID
\ No newline at end of file
diff --git a/src/quackseq/sequences/SE.py b/src/quackseq/sequences/SE.py
new file mode 100644
index 0000000..917f16a
--- /dev/null
+++ b/src/quackseq/sequences/SE.py
@@ -0,0 +1,19 @@
+"""A simple SE sequence with a pi/2 pulse, a pi pulse, and a readout event."""
+
+from quackseq.pulsesequence import QuackSequence
+from quackseq.functions import RectFunction
+
+def create_SE() -> QuackSequence:
+    """Creates a simple SE sequence with a pi/2 pulse, a pi pulse, and a readout event.
+    
+    Returns:
+        QuackSequence: The SE sequence
+    """
+    SE = QuackSequence("SE")
+    SE.add_pulse_event("pi-half", "3u", 100, 0, RectFunction())
+    SE.add_blank_event("te-half", "150u")
+    SE.add_pulse_event("pi", "6u", 100, 0, RectFunction())
+    SE.add_blank_event("blank", "50u")
+    SE.add_readout_event("rx", "200u")
+
+    return SE
\ No newline at end of file
diff --git a/src/quackseq/sequences/SEPC.py b/src/quackseq/sequences/SEPC.py
new file mode 100644
index 0000000..7c4bef5
--- /dev/null
+++ b/src/quackseq/sequences/SEPC.py
@@ -0,0 +1,32 @@
+"""A spin echo sequence with phase cycling."""
+
+from quackseq.pulsesequence import QuackSequence
+from quackseq.functions import RectFunction
+
+def create_SEPC() -> QuackSequence:
+    """Creates a simple spin echo sequence with phase cycling.
+    The sequence consists of a pi/2 pulse, a pi pulse, and a readout event.
+
+    The phase cycling is set to cycle through 0°, 90°, 180°, 270° for the first pulse and constant 180° for the second pulse.
+    The readout phase for the different phase cycles is set to 0°, 90°, 180°, 270°.
+    
+    Returns:
+        QuackSequence: The SEPC sequence
+    """
+    sepc = QuackSequence("SEPC")
+    sepc.add_pulse_event("pi-half", "3u", 100, 0, RectFunction())
+    # This causes the phase to cycle through 0, 90, 180, 270
+    sepc.set_tx_n_phase_cycles("pi-half", 4)
+
+    sepc.add_blank_event("te-half", "150u")
+    # For the second pulse we just need a phase of 180
+    sepc.add_pulse_event("pi", "6u", 100, 180, RectFunction())
+    sepc.add_blank_event("blank", "50u")
+
+    sepc.add_readout_event("rx", "200u")
+    # Readout scheme for phase cycling TX pulses have the scheme 0 90 180 270 for the first pulse and 180 always for the second pulse
+    readout_scheme = [[1, 0], [1, 90], [1, 180], [1, 270]]
+
+    sepc.set_rx_readout_scheme("rx", readout_scheme)
+
+    return sepc
\ No newline at end of file