Skip to content

Refactor trajectory and add colab badges #77

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
ckolbPTB wants to merge 9 commits into
base: main
Choose a base branch
from
Open

Refactor trajectory and add colab badges #77

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
f2c268b
refactor trajectory
ckolbPTB Mar 16, 2026
4710e91
add colab badge
ckolbPTB Mar 16, 2026
42f2fe5
merge main
ckolbPTB Mar 16, 2026
02c3c8e
reduce example install
ckolbPTB Mar 16, 2026
18acedb
install dev for building example documentation
ckolbPTB Mar 16, 2026
444d6ff
rename sequences
ckolbPTB Mar 17, 2026
784b516
move set def to kernels
ckolbPTB Mar 23, 2026
2d7d5b5
Merge branch 'main' into refactor_trajectory
schuenke Mar 26, 2026
ab1299f
Merge branch 'main' into refactor_trajectory
schuenke Apr 27, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion .github/dependabot.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ updates:
- package-ecosystem: "github-actions"
directory: "/"
schedule:
interval: "daily"
interval: "monthly"
groups:
all-actions:
patterns: ["*"]
2 changes: 1 addition & 1 deletion .github/workflows/examples.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ jobs:
run: |
pip install --index-url=https://download.pytorch.org/whl/cpu \
--extra-index-url https://pypi.org/simple/ \
--upgrade --upgrade-strategy eager -e .[examples]
--upgrade --upgrade-strategy eager -e .[dev]

# Build the book
- name: Build the book
Expand Down
2 changes: 1 addition & 1 deletion examples/grpe_flash_dixon.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@
"from mrpro.operators.models import SpoiledGRE\n",
"from scipy.interpolate import interp1d\n",
"\n",
"from mrseq.scripts.grpe_flash_dixon import main as create_seq\n",
"from mrseq.sequences.grpe_flash_dixon import main as create_seq\n",
"from mrseq.utils import combine_ismrmrd_files\n",
"from mrseq.utils import sys_defaults"
]
Expand Down
53 changes: 37 additions & 16 deletions examples/radial_flash.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,14 @@
"cell_type": "markdown",
"id": "0",
"metadata": {},
"source": [
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PTB-MR/mrseq/blob/main/examples/radial_flash.ipynb)"
]
},
{
"cell_type": "markdown",
"id": "1",
"metadata": {},
"source": [
"# Radial FLASH\n",
"\n",
Expand All @@ -12,7 +20,7 @@
},
{
"cell_type": "markdown",
"id": "1",
"id": "2",
"metadata": {},
"source": [
"### Imports"
Expand All @@ -21,7 +29,20 @@
{
"cell_type": "code",
"execution_count": null,
"id": "2",
"id": "3",
"metadata": {},
"outputs": [],
"source": [
"import importlib\n",
"\n",
"if not importlib.util.find_spec('mrseq'):\n",
" %pip install mrseq[examples]"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "4",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -37,14 +58,14 @@
"from mrpro.data.traj_calculators import KTrajectoryIsmrmrd\n",
"from mrpro.operators.models import SpoiledGRE\n",
"\n",
"from mrseq.scripts.radial_flash import main as create_seq\n",
"from mrseq.sequences.radial_flash import main as create_seq\n",
"from mrseq.utils import combine_ismrmrd_files\n",
"from mrseq.utils import sys_defaults"
]
},
{
"cell_type": "markdown",
"id": "3",
"id": "5",
"metadata": {},
"source": [
"### Settings\n",
Expand All @@ -55,7 +76,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "4",
"id": "6",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -69,7 +90,7 @@
},
{
"cell_type": "markdown",
"id": "5",
"id": "7",
"metadata": {},
"source": [
"### Create the digital phantom\n",
Expand All @@ -80,7 +101,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "6",
"id": "8",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -90,7 +111,7 @@
},
{
"cell_type": "markdown",
"id": "7",
"id": "9",
"metadata": {},
"source": [
"### Create the radial FLASH sequence\n",
Expand All @@ -101,7 +122,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "8",
"id": "10",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -119,7 +140,7 @@
},
{
"cell_type": "markdown",
"id": "9",
"id": "11",
"metadata": {},
"source": [
"### Simulate the sequence\n",
Expand All @@ -130,7 +151,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "10",
"id": "12",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -142,7 +163,7 @@
},
{
"cell_type": "markdown",
"id": "11",
"id": "13",
"metadata": {},
"source": [
"### Reconstruct the image\n",
Expand All @@ -152,7 +173,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "12",
"id": "14",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -163,7 +184,7 @@
},
{
"cell_type": "markdown",
"id": "13",
"id": "15",
"metadata": {},
"source": [
"### Compare to theoretical model\n",
Expand All @@ -174,7 +195,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "14",
"id": "16",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -184,7 +205,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "15",
"id": "17",
"metadata": {},
"outputs": [],
"source": [
Expand Down
53 changes: 37 additions & 16 deletions examples/spiral_flash.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,14 @@
"cell_type": "markdown",
"id": "0",
"metadata": {},
"source": [
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/PTB-MR/mrseq/blob/main/examples/spiral_flash.ipynb)"
]
},
{
"cell_type": "markdown",
"id": "1",
"metadata": {},
"source": [
"# Spiral FLASH\n",
"\n",
Expand All @@ -12,7 +20,7 @@
},
{
"cell_type": "markdown",
"id": "1",
"id": "2",
"metadata": {},
"source": [
"### Imports"
Expand All @@ -21,7 +29,20 @@
{
"cell_type": "code",
"execution_count": null,
"id": "2",
"id": "3",
"metadata": {},
"outputs": [],
"source": [
"import importlib\n",
"\n",
"if not importlib.util.find_spec('mrseq'):\n",
" %pip install mrseq[examples]"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "4",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -37,14 +58,14 @@
"from mrpro.data.traj_calculators import KTrajectoryIsmrmrd\n",
"from mrpro.operators.models import SpoiledGRE\n",
"\n",
"from mrseq.scripts.spiral_flash import main as create_seq\n",
"from mrseq.sequences.spiral_flash import main as create_seq\n",
"from mrseq.utils import combine_ismrmrd_files\n",
"from mrseq.utils import sys_defaults"
]
},
{
"cell_type": "markdown",
"id": "3",
"id": "5",
"metadata": {},
"source": [
"### Settings\n",
Expand All @@ -55,7 +76,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "4",
"id": "6",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -69,7 +90,7 @@
},
{
"cell_type": "markdown",
"id": "5",
"id": "7",
"metadata": {},
"source": [
"### Create the digital phantom\n",
Expand All @@ -80,7 +101,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "6",
"id": "8",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -90,7 +111,7 @@
},
{
"cell_type": "markdown",
"id": "7",
"id": "9",
"metadata": {},
"source": [
"### Create the spiral FLASH sequence\n",
Expand All @@ -101,7 +122,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "8",
"id": "10",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -119,7 +140,7 @@
},
{
"cell_type": "markdown",
"id": "9",
"id": "11",
"metadata": {},
"source": [
"### Simulate the sequence\n",
Expand All @@ -130,7 +151,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "10",
"id": "12",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -142,7 +163,7 @@
},
{
"cell_type": "markdown",
"id": "11",
"id": "13",
"metadata": {},
"source": [
"### Reconstruct the image\n",
Expand All @@ -152,7 +173,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "12",
"id": "14",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -163,7 +184,7 @@
},
{
"cell_type": "markdown",
"id": "13",
"id": "15",
"metadata": {},
"source": [
"### Compare to theoretical model\n",
Expand All @@ -174,7 +195,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "14",
"id": "16",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -184,7 +205,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "15",
"id": "17",
"metadata": {},
"outputs": [],
"source": [
Expand Down
Loading
Loading