Merge branch 'main' into coilcompress

PTB-MR · Nov 7, 2024 · 3cdeafb · 3cdeafb
2 parents f36b1dd + bc830f5
commit 3cdeafb
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,7 +3,7 @@
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-added-large-files
       - id: check-docstring-first
@@ -15,14 +15,14 @@ repos:
       - id: mixed-line-ending
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.9
+    rev: v0.7.2
     hooks:
       - id: ruff # linter
         args: [--fix]
       - id: ruff-format # formatter
 
   - repo: https://github.com/crate-ci/typos
-    rev: v1.25.0
+    rev: v1.27.0
     hooks:
       - id: typos
 
@@ -34,7 +34,7 @@ repos:
         exclude: ^tests/
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.2
+    rev: v1.13.0
     hooks:
       - id: mypy
         pass_filenames: false

diff --git a/examples/direct_reconstruction.ipynb b/examples/direct_reconstruction.ipynb
@@ -37,10 +37,10 @@
     "\n",
     "import requests\n",
     "\n",
-    "data_file = tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5')\n",
-    "response = requests.get(zenodo_url + fname, timeout=30)\n",
-    "data_file.write(response.content)\n",
-    "data_file.flush()"
+    "with tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5') as data_file:\n",
+    "    response = requests.get(zenodo_url + fname, timeout=30)\n",
+    "    data_file.write(response.content)\n",
+    "    data_file.flush()"
    ]
   },
   {

diff --git a/examples/direct_reconstruction.py b/examples/direct_reconstruction.py
@@ -11,10 +11,10 @@
 
 import requests
 
-data_file = tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5')
-response = requests.get(zenodo_url + fname, timeout=30)
-data_file.write(response.content)
-data_file.flush()
+with tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5') as data_file:
+    response = requests.get(zenodo_url + fname, timeout=30)
+    data_file.write(response.content)
+    data_file.flush()
 
 # %% [markdown]
 # ### Image reconstruction

diff --git a/examples/iterative_sense_reconstruction.ipynb b/examples/iterative_sense_reconstruction.ipynb
@@ -37,10 +37,10 @@
     "\n",
     "import requests\n",
     "\n",
-    "data_file = tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5')\n",
-    "response = requests.get(zenodo_url + fname, timeout=30)\n",
-    "data_file.write(response.content)\n",
-    "data_file.flush()"
+    "with tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5') as data_file:\n",
+    "    response = requests.get(zenodo_url + fname, timeout=30)\n",
+    "    data_file.write(response.content)\n",
+    "    data_file.flush()"
    ]
   },
   {

diff --git a/examples/iterative_sense_reconstruction.py b/examples/iterative_sense_reconstruction.py
@@ -11,10 +11,10 @@
 
 import requests
 
-data_file = tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5')
-response = requests.get(zenodo_url + fname, timeout=30)
-data_file.write(response.content)
-data_file.flush()
+with tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5') as data_file:
+    response = requests.get(zenodo_url + fname, timeout=30)
+    data_file.write(response.content)
+    data_file.flush()
 
 # %% [markdown]
 # ### Image reconstruction

diff --git a/examples/pulseq_2d_radial_golden_angle.ipynb b/examples/pulseq_2d_radial_golden_angle.ipynb
@@ -33,13 +33,14 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "d16f41f1",
-   "metadata": {},
+   "metadata": {
+    "lines_to_next_cell": 2
+   },
    "outputs": [],
    "source": [
     "# define zenodo records URL and create a temporary directory and h5-file\n",
     "zenodo_url = 'https://zenodo.org/records/10854057/files/'\n",
-    "fname = 'pulseq_radial_2D_402spokes_golden_angle_with_traj.h5'\n",
-    "data_file = tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5')"
+    "fname = 'pulseq_radial_2D_402spokes_golden_angle_with_traj.h5'"
    ]
   },
   {
@@ -50,9 +51,10 @@
    "outputs": [],
    "source": [
     "# Download raw data using requests\n",
-    "response = requests.get(zenodo_url + fname, timeout=30)\n",
-    "data_file.write(response.content)\n",
-    "data_file.flush()"
+    "with tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5') as data_file:\n",
+    "    response = requests.get(zenodo_url + fname, timeout=30)\n",
+    "    data_file.write(response.content)\n",
+    "    data_file.flush()"
    ]
   },
   {
@@ -125,10 +127,10 @@
     "# download the sequence file from zenodo\n",
     "zenodo_url = 'https://zenodo.org/records/10868061/files/'\n",
     "seq_fname = 'pulseq_radial_2D_402spokes_golden_angle.seq'\n",
-    "seq_file = tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.seq')\n",
-    "response = requests.get(zenodo_url + seq_fname, timeout=30)\n",
-    "seq_file.write(response.content)\n",
-    "seq_file.flush()"
+    "with tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.seq') as seq_file:\n",
+    "    response = requests.get(zenodo_url + seq_fname, timeout=30)\n",
+    "    seq_file.write(response.content)\n",
+    "    seq_file.flush()"
    ]
   },
   {

diff --git a/examples/pulseq_2d_radial_golden_angle.py b/examples/pulseq_2d_radial_golden_angle.py
@@ -19,13 +19,14 @@
 # define zenodo records URL and create a temporary directory and h5-file
 zenodo_url = 'https://zenodo.org/records/10854057/files/'
 fname = 'pulseq_radial_2D_402spokes_golden_angle_with_traj.h5'
-data_file = tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5')
+
 
 # %%
 # Download raw data using requests
-response = requests.get(zenodo_url + fname, timeout=30)
-data_file.write(response.content)
-data_file.flush()
+with tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5') as data_file:
+    response = requests.get(zenodo_url + fname, timeout=30)
+    data_file.write(response.content)
+    data_file.flush()
 
 # %% [markdown]
 # ### Image reconstruction using KTrajectoryIsmrmrd
@@ -62,10 +63,10 @@
 # download the sequence file from zenodo
 zenodo_url = 'https://zenodo.org/records/10868061/files/'
 seq_fname = 'pulseq_radial_2D_402spokes_golden_angle.seq'
-seq_file = tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.seq')
-response = requests.get(zenodo_url + seq_fname, timeout=30)
-seq_file.write(response.content)
-seq_file.flush()
+with tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.seq') as seq_file:
+    response = requests.get(zenodo_url + seq_fname, timeout=30)
+    seq_file.write(response.content)
+    seq_file.flush()
 
 # %%
 # Read raw data and calculate trajectory using KTrajectoryPulseq