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fix styling. #3

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Merged
mcencini merged 1 commit into from
Feb 12, 2025
Merged

fix styling. #3

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11 changes: 3 additions & 8 deletions src/pypulseq/Sequence/block.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,6 @@

import numpy as np

from pypulseq import eps
from pypulseq.block_to_events import block_to_events
from pypulseq.compress_shape import compress_shape
from pypulseq.decompress_shape import decompress_shape
Expand Down Expand Up @@ -148,10 +147,7 @@ def set_block(self, block_index: int, *args: SimpleNamespace) -> None:
else:
event_id = register_rotation_event(self, event)

ext = {
'type': self.get_extension_type_ID('ROTATIONS'),
'ref': event_id
}
ext = {'type': self.get_extension_type_ID('ROTATIONS'), 'ref': event_id}
extensions.append(ext)
elif event.type in ['labelset', 'labelinc']:
if hasattr(event, 'id'):
Expand Down Expand Up @@ -205,7 +201,6 @@ def set_block(self, block_index: int, *args: SimpleNamespace) -> None:
# PERFORM GRADIENT CHECKS
# =========
grad_check(self, block_index, check_g, duration, rot_event)


self.block_events[block_index] = new_block
self.block_durations[block_index] = float(duration)
Expand Down Expand Up @@ -353,10 +348,10 @@ def get_block(self, block_index: int) -> SimpleNamespace:
block.trigger[len(block.trigger)] = trigger
else:
block.trigger = {0: trigger}
elif ext_type == "ROTATIONS":
elif ext_type == 'ROTATIONS':
data = self.rotation_library.data[ext_data[1]]
rotation = SimpleNamespace()
rotation.type = "rotation"
rotation.type = 'rotation'
rotation.rot_matrix = np.asarray(data).reshape(3, 3)
block.rotation = rotation
elif ext_type in ['LABELSET', 'LABELINC']:
Expand Down
129 changes: 43 additions & 86 deletions src/pypulseq/Sequence/grad_check.py
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Original file line number Diff line number Diff line change
Expand Up @@ -65,13 +65,10 @@ def grad_check_norot(self, block_index, check_g, duration):
"""
for grad_to_check in check_g.values():
if (
abs(grad_to_check.start[1])
> self.system.max_slew * self.system.grad_raster_time
): # noqa: SIM102
if grad_to_check.start[0] > eps:
raise RuntimeError(
"No delay allowed for gradients which start with a non-zero amplitude"
)
abs(grad_to_check.start[1]) > self.system.max_slew * self.system.grad_raster_time
and grad_to_check.start[0] > eps
):
raise RuntimeError('No delay allowed for gradients which start with a non-zero amplitude')

# Check whether any blocks exist in the sequence
if self.next_free_block_ID > 1:
Expand All @@ -86,9 +83,7 @@ def grad_check_norot(self, block_index, check_g, duration):
# Existing block overwritten
idx = blocks.index(block_index)
prev_block_index = blocks[idx - 1] if idx > 0 else None
next_block_index = (
blocks[idx + 1] if idx < len(blocks) - 1 else None
)
next_block_index = blocks[idx + 1] if idx < len(blocks) - 1 else None
except ValueError:
# Inserting a new block with non-contiguous numbering
prev_block_index = next(reversed(self.block_events))
Expand All @@ -100,66 +95,50 @@ def grad_check_norot(self, block_index, check_g, duration):
prev_id = self.block_events[prev_block_index][grad_to_check.idx]
if prev_id != 0:
prev_lib = self.grad_library.get(prev_id)
prev_type = prev_lib["type"]
prev_type = prev_lib['type']

if prev_type == "t":
if prev_type == 't':
last = 0
elif prev_type == "g":
last = prev_lib["data"][5]
elif prev_type == 'g':
last = prev_lib['data'][5]

# Check whether the difference between the last gradient value and
# the first value of the new gradient is achievable with the
# specified slew rate.
if (
abs(last - grad_to_check.start[1])
> self.system.max_slew * self.system.grad_raster_time
):
raise RuntimeError(
"Two consecutive gradients need to have the same amplitude at the connection point"
)
if abs(last - grad_to_check.start[1]) > self.system.max_slew * self.system.grad_raster_time:
raise RuntimeError('Two consecutive gradients need to have the same amplitude at the connection point')

# Look up the first gradient value in the next block
# (this only happens when using set_block to patch a block)
if next_block_index is not None:
next_id = self.block_events[next_block_index][grad_to_check.idx]
if next_id != 0:
next_lib = self.grad_library.get(next_id)
next_type = next_lib["type"]
next_type = next_lib['type']

if next_type == "t":
if next_type == 't':
first = 0
elif next_type == "g":
first = next_lib["data"][4]
elif next_type == 'g':
first = next_lib['data'][4]
else:
first = 0

# Check whether the difference between the first gradient value
# in the next block and the last value of the new gradient is
# achievable with the specified slew rate.
if (
abs(first - grad_to_check.stop[1])
> self.system.max_slew * self.system.grad_raster_time
):
if abs(first - grad_to_check.stop[1]) > self.system.max_slew * self.system.grad_raster_time:
raise RuntimeError(
"Two consecutive gradients need to have the same amplitude at the connection point"
'Two consecutive gradients need to have the same amplitude at the connection point'
)
elif (
abs(grad_to_check.start[1])
> self.system.max_slew * self.system.grad_raster_time
):
raise RuntimeError(
"First gradient in the the first block has to start at 0."
)
elif abs(grad_to_check.start[1]) > self.system.max_slew * self.system.grad_raster_time:
raise RuntimeError('First gradient in the the first block has to start at 0.')

# Check if gradients, which do not end at 0, are as long as the block itself.
if (
abs(grad_to_check.stop[1])
> self.system.max_slew * self.system.grad_raster_time
abs(grad_to_check.stop[1]) > self.system.max_slew * self.system.grad_raster_time
and abs(grad_to_check.stop[0] - duration) > 1e-7
):
raise RuntimeError(
"A gradient that doesn't end at zero needs to be aligned to the block boundary."
)
raise RuntimeError("A gradient that doesn't end at zero needs to be aligned to the block boundary.")


def grad_check_rot(self, block_index, check_g, duration, rot_event):
Expand Down Expand Up @@ -193,13 +172,10 @@ def grad_check_rot(self, block_index, check_g, duration, rot_event):
for grad_to_check in check_g.values():
# Check beginning of gradient event
if (
abs(grad_to_check.start[1])
> self.system.max_slew * self.system.grad_raster_time
): # noqa: SIM102
if grad_to_check.start[0] > eps:
raise RuntimeError(
"No delay allowed for gradients which start with a non-zero amplitude"
)
abs(grad_to_check.start[1]) > self.system.max_slew * self.system.grad_raster_time
and grad_to_check.start[0] > eps
):
raise RuntimeError('No delay allowed for gradients which start with a non-zero amplitude')

# Check whether any blocks exist in the sequence
if self.next_free_block_ID > 1:
Expand All @@ -208,7 +184,7 @@ def grad_check_rot(self, block_index, check_g, duration, rot_event):
next_has_rot = False

# Rotation extension ID
rot_type_id = self.get_extension_type_ID("ROTATIONS")
rot_type_id = self.get_extension_type_ID('ROTATIONS')

# Get indexes of previous and next blocks
if block_index == self.next_free_block_ID:
Expand All @@ -235,13 +211,13 @@ def grad_check_rot(self, block_index, check_g, duration, rot_event):
prev_id = self.block_events[prev_block_index][grad_to_check.idx]
if prev_id != 0:
prev_lib = self.grad_library.get(prev_id)
prev_type = prev_lib["type"]
prev_type = prev_lib['type']

# Trapezoids end with zeros,
# so we cannot have the same amplitude
# as the initial value of current block
if prev_type == "g":
prev_grad_last[grad_to_check.idx - 2] = prev_lib["data"][5]
if prev_type == 'g':
prev_grad_last[grad_to_check.idx - 2] = prev_lib['data'][5]

# Get previous block rotation matrix
ext_id = self.block_events[prev_block_index][-1]
Expand All @@ -250,9 +226,7 @@ def grad_check_rot(self, block_index, check_g, duration, rot_event):
ext = self.extensions_library.data.get(ext_id)
if ext[0] == rot_type_id:
previous_has_rot = True
previous_rotmat = np.asarray(
self.rotation_library.data.get(ext[1])
).reshape((3, 3))
previous_rotmat = np.asarray(self.rotation_library.data.get(ext[1])).reshape((3, 3))
else:
ext_id = ext[-1]
except KeyError:
Expand All @@ -272,30 +246,26 @@ def grad_check_rot(self, block_index, check_g, duration, rot_event):
curr_grad_first = rot_event.rot_matrix @ curr_grad_first

# Compare current block with previous
if any(
abs(curr_grad_first - prev_grad_last)
> self.system.max_slew * self.system.grad_raster_time
):
if any(abs(curr_grad_first - prev_grad_last) > self.system.max_slew * self.system.grad_raster_time):
raise RuntimeError(
f"Error in block {block_index}: Two consecutive gradients need to have the same amplitude at the connection point."
f'Error in block {block_index}: Two consecutive gradients need to have the same amplitude at the connection point.'
)

# 2) Comparison with next block
if next_block_index is not None:

# Look up the last gradient value in the previous block
next_grad_first = np.zeros(3, dtype=np.float32)
for grad_to_check in check_g.values():
next_id = self.block_events[next_block_index][grad_to_check.idx]
if next_id != 0:
next_lib = self.grad_library.get(next_id)
next_type = next_lib["type"]
next_type = next_lib['type']

# Trapezoids start with zeros,
# so we cannot have the same amplitude
# as the final value of current block
if next_type == "g":
next_grad_first[grad_to_check.idx - 2] = next_lib["data"][4]
if next_type == 'g':
next_grad_first[grad_to_check.idx - 2] = next_lib['data'][4]

# Get next block rotation matrix
ext_id = self.block_events[next_block_index][-1]
Expand All @@ -304,9 +274,7 @@ def grad_check_rot(self, block_index, check_g, duration, rot_event):
ext = self.extensions_library.data.get(ext_id)
if ext[0] == rot_type_id:
next_has_rot = True
next_rotmat = np.asarray(
self.rotation_library.data.get(ext[1])
).reshape((3, 3))
next_rotmat = np.asarray(self.rotation_library.data.get(ext[1])).reshape((3, 3))
else:
ext_id = ext[-1]
except KeyError:
Expand All @@ -326,31 +294,20 @@ def grad_check_rot(self, block_index, check_g, duration, rot_event):
curr_grad_last = rot_event.rot_matrix @ curr_grad_last

# Compare current block with next
if any(
abs(curr_grad_last - next_grad_first)
> self.system.max_slew * self.system.grad_raster_time
):
if any(abs(curr_grad_last - next_grad_first) > self.system.max_slew * self.system.grad_raster_time):
raise RuntimeError(
f"Error in block {block_index}: Two consecutive gradients need to have the same amplitude at the connection point."
f'Error in block {block_index}: Two consecutive gradients need to have the same amplitude at the connection point.'
)
else:
for grad_to_check in check_g.values():
# Check beginning of gradient event
if (
abs(grad_to_check.start[1])
> self.system.max_slew * self.system.grad_raster_time
):
raise RuntimeError(
"First gradient in the the first block has to start at 0."
)
if abs(grad_to_check.start[1]) > self.system.max_slew * self.system.grad_raster_time:
raise RuntimeError('First gradient in the the first block has to start at 0.')

# Check if gradients, which do not end at 0, are as long as the block itself.
for grad_to_check in check_g.values():
if (
abs(grad_to_check.stop[1])
> self.system.max_slew * self.system.grad_raster_time
abs(grad_to_check.stop[1]) > self.system.max_slew * self.system.grad_raster_time
and abs(grad_to_check.stop[0] - duration) > 1e-7
):
if abs(grad_to_check.stop[0] - duration) > 1e-7:
raise RuntimeError(
"A gradient that doesn't end at zero needs to be aligned to the block boundary."
)
raise RuntimeError("A gradient that doesn't end at zero needs to be aligned to the block boundary.")
4 changes: 2 additions & 2 deletions src/pypulseq/Sequence/read_seq.py
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Original file line number Diff line number Diff line change
Expand Up @@ -167,9 +167,9 @@ def read(self, path: str, detect_rf_use: bool = False, remove_duplicates: bool =
extension_id = int(section[18:])
self.set_extension_string_ID('TRIGGERS', extension_id)
self.trigger_library = __read_events(input_file, (1, 1, 1e-6, 1e-6), event_library=self.trigger_library)
elif section[:19] == "extension ROTATIONS":
elif section[:19] == 'extension ROTATIONS':
extension_id = int(section[19:])
self.set_extension_string_ID("ROTATIONS", extension_id)
self.set_extension_string_ID('ROTATIONS', extension_id)
self.rotation_library = __read_events(
input_file, (1, 1, 1, 1, 1, 1, 1, 1, 1), event_library=self.rotation_library
)
Expand Down
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