Switch from jupyternotebook to jupyterlab

NicoleJurjew · Jan 20, 2023 · a42ca6b · a42ca6b
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diff --git a/DocForInstructors.md b/DocForInstructors.md
@@ -13,7 +13,7 @@ This is a basic list of things to do and tell people during the course.
   update_VM.sh # if required
   cd ~/devel/SIRF-Exercises/
   scripts/download_data.sh -m -p
-  jupyter notebook
+  jupyter lab
   ```
   Then open a web-browser on your local laptop and point it to http://localhost:8888 (fill in the password or the token).
 
@@ -24,15 +24,13 @@ Then open a web-browser on your local laptop and point it to http://localhost:99
 
 ## Basic jupyter notebook manipulations
 1. Open notebook and tell them about execution and keyboard shortcuts (via menu).
-2. Warn that closing the tab leaves a python session running. This can be surprising (for instance with read/write access).
-Show how to close the session (either `File->Close and halt` or go "home" and click on the `Running` tab.
-3. Show how to create a terminal ("home", `New` on the right, `Terminal`). Use this to start the Gadgetron. Say this is not necessary on Docker as already started.
+3. Show how to create a terminal ("Launcher" (or first "+"), `Terminal`). Use this to start the Gadgetron. Say this is not necessary on Docker as already started.
    ```bash
    gadgetron&
    ```
 4. Warn that you cannot have 2 Python sessions simultaneously accessing
 the same MR HDF5 file.
-The only work-around is to use “File->Close and halt”  after you’ve finished with a notebook (or just “Kernel->Shutdown”).
+The only work-around is to use “kernel -> "Shutdown kernel" in one notebook, or close it).
 
 5. Warn that pressing `Logout` will mean all sessions are closed and you will have to start again. Warn that pressing
 `Quit` means the server will quit and they will be in trouble. (On Azure, the server should restart after a few seconds,

diff --git a/DocForParticipants.md b/DocForParticipants.md
@@ -56,6 +56,12 @@ The next sections contain instructions to start the Jupyter notebook server with
 
 ## Start a jupyter notebook server for the SIRF exercises
 
+***Warning:** these instructions are when using JupyterLab as opposed to the "classic" notebook
+interface. If you choose to use the classic interface, you will have to modify the notebooks
+marginally by replacing `%matplotlib widget` with `%matplotlib notebook`.
+See also the [iPython section](#ipython) below.
+
+
 ### Using an Azure client (if available)
 
 The web-address should be something like https://sirf1....cloudapp.azure.com:9999/. See local instructions of your training sessoin.
@@ -75,15 +81,15 @@ Follow instructions given elsewhere.
   ```bash
   # optionally update to the latest release of SIRF and the SIRF-Exercises
   update_VM.sh
-  jupyter notebook
+  jupyter lab
   ```
 
 Then open a web-browser on your computer (i.e. the host) and point it to http://localhost:8888 (fill in the password or the token).
 
 If this fails, you could try to use web browser in the VM instead.
 ```bash
    sudo apt install firefox
-   jupyter notebook --browser firefox
+   jupyter lab --browser firefox
 ```
 
 ### Using Docker
@@ -98,7 +104,7 @@ Please note that for at present (at least up to SIRF 3.4), you need to point you
 You have a jupyter server (as you followed the [installation instructions](INSTALL.md)) so just use
    ```bash
    cd /wherever/you/installed/it/SIRF-Exercises
-   jupyter notebook
+   jupyter lab
    ```
 
 ## Starting a terminal via Jupyter

diff --git a/INSTALL.md b/INSTALL.md
@@ -41,7 +41,8 @@ sure that you use a Python version which is compatible with how you compiled SIR
 
 Of course, if you've used (Ana)conda to install Python etc (and are sure
 SIRF was compiled with that Python version), you can use conda to install
-dependencies as well. Or you could still choose to use conda's `pip` after
+dependencies as well (except the brainweb module, at the time of writing).
+Or you could still choose to use conda's `pip` after
 
     conda install pip
 

diff --git a/notebooks/Geometry/c_fully3dgeom.ipynb b/notebooks/Geometry/c_fully3dgeom.ipynb
@@ -57,7 +57,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%matplotlib notebook"
+    "%matplotlib widget"
    ]
   },
   {

diff --git a/notebooks/Geometry/d_manipulation.ipynb b/notebooks/Geometry/d_manipulation.ipynb
@@ -76,7 +76,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%matplotlib notebook"
+    "%matplotlib widget"
    ]
   },
   {

diff --git a/notebooks/Introductory/acquisition_model_mr_pet_ct.ipynb b/notebooks/Introductory/acquisition_model_mr_pet_ct.ipynb
@@ -46,7 +46,7 @@
    "outputs": [],
    "source": [
     "# Make sure figures appears inline and animations works\n",
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "import notebook_setup\n",
     "from sirf_exercises import cd_to_working_dir\n",
     "cd_to_working_dir('Introductory', 'acquisition_model_mr_pet_ct')"

diff --git a/notebooks/Introductory/introduction.ipynb b/notebooks/Introductory/introduction.ipynb
@@ -46,7 +46,8 @@
    "outputs": [],
    "source": [
     "# Make sure figures appears inline and animations works\n",
-    "%matplotlib notebook"
+    "# Edit this to \"\"%matplotlib notebook\" when using the \"classic\" jupyter notebook interface\n",
+    "%matplotlib widget"
    ]
   },
   {
@@ -803,5 +804,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }
diff --git a/notebooks/MR/Old_notebooks/Gadgetron/fully_sampled_recon_single_chain.ipynb b/notebooks/MR/Old_notebooks/Gadgetron/fully_sampled_recon_single_chain.ipynb
@@ -41,7 +41,7 @@
     "# import engine module\n",
     "from sirf.Gadgetron import *\n",
     "\n",
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "\n",
     "# process command-line options\n",
     "data_file = 'simulated_MR_2D_cartesian.h5' \n",

diff --git a/notebooks/MR/Old_notebooks/fully_sampled_recon.ipynb b/notebooks/MR/Old_notebooks/fully_sampled_recon.ipynb
@@ -38,7 +38,7 @@
     "\n",
     "# import engine module\n",
     "#exec('from p' + args['--engine'] + ' import *')\n",
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "from sirf.Gadgetron import *\n",
     "\n",
     "# Simulated Data\n",

diff --git a/notebooks/MR/Old_notebooks/grappa_basic.ipynb b/notebooks/MR/Old_notebooks/grappa_basic.ipynb
@@ -54,7 +54,7 @@
     "#__version__ = '0.1.0'\n",
     "from docopt import docopt\n",
     "#args = docopt(__doc__, version=__version__)\n",
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "# import engine module\n",
     "#exec('from p' + args['--engine'] + ' import *')\n",
     "from sirf.Gadgetron import *\n",

diff --git a/notebooks/MR/a_fully_sampled.ipynb b/notebooks/MR/a_fully_sampled.ipynb
@@ -148,7 +148,7 @@
    "outputs": [],
    "source": [
     "#%% make sure figures appears inline and animations works\n",
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "\n",
     "# Setup the working directory for the notebook\n",
     "import notebook_setup\n",

diff --git a/notebooks/MR/b_kspace_filter.ipynb b/notebooks/MR/b_kspace_filter.ipynb
@@ -41,7 +41,7 @@
    "outputs": [],
    "source": [
     "#%% make sure figures appears inline and animations works\n",
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "\n",
     "# Setup the working directory for the notebook\n",
     "import notebook_setup\n",

diff --git a/notebooks/MR/c_coil_combination.ipynb b/notebooks/MR/c_coil_combination.ipynb
@@ -40,7 +40,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "\n",
     "# Setup the working directory for the notebook\n",
     "import notebook_setup\n",

diff --git a/notebooks/MR/d_undersampled_reconstructions.ipynb b/notebooks/MR/d_undersampled_reconstructions.ipynb
@@ -42,7 +42,7 @@
    "outputs": [],
    "source": [
     "#%% make sure figures appears inline and animations works\n",
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "\n",
     "# Setup the working directory for the notebook\n",
     "import notebook_setup\n",

diff --git a/notebooks/MR/e_advanced_recon.ipynb b/notebooks/MR/e_advanced_recon.ipynb
@@ -48,7 +48,7 @@
    "outputs": [],
    "source": [
     "#%% make sure figures appears inline and animations works\n",
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "\n",
     "# Setup the working directory for the notebook\n",
     "import notebook_setup\n",

diff --git a/notebooks/MR/f_create_undersampled_kspace.ipynb b/notebooks/MR/f_create_undersampled_kspace.ipynb
@@ -75,7 +75,7 @@
    "outputs": [],
    "source": [
     "#%% make sure figures appears inline and animations works\n",
-    "%matplotlib notebook"
+    "%matplotlib widget"
    ]
   },
   {

diff --git a/notebooks/MR/tools/acqh5info.ipynb b/notebooks/MR/tools/acqh5info.ipynb
@@ -31,7 +31,7 @@
     "slc = acq_cont.get_ISMRMRD_info('slice')\n",
     "rep = acq_cont.get_ISMRMRD_info('repetition')\n",
     "\n",
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "\n",
     "plt.plot(ec1, label='enc 1')\n",
     "plt.plot(ec2, label='enc 2')\n",

diff --git a/notebooks/MR/tools/im5info.ipynb b/notebooks/MR/tools/im5info.ipynb
@@ -47,7 +47,7 @@
     "# Set output based on shape returned above\n",
     "img = dset[2,0,0,:,:]\n",
     "\n",
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "\n",
     "plt.imshow(img, cmap='gray')\n",
     "plt.colorbar()\n"

diff --git a/notebooks/PET/DIY_OSEM.ipynb b/notebooks/PET/DIY_OSEM.ipynb
@@ -41,7 +41,7 @@
    "outputs": [],
    "source": [
     "#%% make sure figures appears inline and animations works\n",
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "\n",
     "# Setup the working directory for the notebook\n",
     "import notebook_setup\n",

diff --git a/notebooks/PET/MAPEM.ipynb b/notebooks/PET/MAPEM.ipynb
@@ -76,7 +76,7 @@
    "outputs": [],
    "source": [
     "#%% make sure figures appears inline and animations works\n",
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "\n",
     "# Setup the working directory for the notebook\n",
     "import notebook_setup\n",

diff --git a/notebooks/PET/ML_reconstruction.ipynb b/notebooks/PET/ML_reconstruction.ipynb
@@ -62,7 +62,7 @@
    "outputs": [],
    "source": [
     "#%% make sure figures appears inline and animations works\n",
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "\n",
     "# Setup the working directory for the notebook\n",
     "import notebook_setup\n",

diff --git a/notebooks/PET/OSEM_reconstruction.ipynb b/notebooks/PET/OSEM_reconstruction.ipynb
@@ -53,7 +53,7 @@
    "outputs": [],
    "source": [
     "#%% make sure figures appears inline and animations works\n",
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "\n",
     "# Setup the working directory for the notebook\n",
     "import notebook_setup\n",

diff --git a/notebooks/PET/display_and_projection.ipynb b/notebooks/PET/display_and_projection.ipynb
@@ -58,7 +58,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%matplotlib notebook"
+    "%matplotlib widget"
    ]
   },
   {
@@ -285,7 +285,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Note that when using the `%matplotlib notebook` or `inline` back-ends, the `title` is currently not shown when using `show`. Apologies"
+    "Note that when using the `%matplotlib widget` or `inline` back-ends, the `title` is currently not shown when using `show`. Apologies"
    ]
   },
   {

diff --git a/notebooks/PET/image_creation_and_simulation.ipynb b/notebooks/PET/image_creation_and_simulation.ipynb
@@ -47,7 +47,7 @@
    "outputs": [],
    "source": [
     "#%% make sure figures appears inline and animations works\n",
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "\n",
     "# Setup the working directory for the notebook\n",
     "import notebook_setup\n",

diff --git a/notebooks/PET/reconstruct_measured_data.ipynb b/notebooks/PET/reconstruct_measured_data.ipynb
@@ -53,7 +53,7 @@
    "outputs": [],
    "source": [
     "#%% make sure figures appears inline and animations works\n",
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "\n",
     "# Setup the working directory for the notebook\n",
     "import notebook_setup\n",

diff --git a/notebooks/Reg/sirf_registration.ipynb b/notebooks/Reg/sirf_registration.ipynb
@@ -51,7 +51,7 @@
    "outputs": [],
    "source": [
     "#%% make sure figures appears inline and animations works\n",
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "\n",
     "# Setup the working directory for the notebook\n",
     "import notebook_setup\n",

diff --git a/notebooks/Synergistic/BrainWeb-single_slice_motion.ipynb b/notebooks/Synergistic/BrainWeb-single_slice_motion.ipynb
@@ -33,7 +33,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "\n",
     "# Setup the working directory for the notebook\n",
     "import notebook_setup\n",

diff --git a/notebooks/Synergistic/BrainWeb.ipynb b/notebooks/Synergistic/BrainWeb.ipynb
@@ -52,7 +52,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "\n",
     "# Setup the working directory for the notebook\n",
     "import notebook_setup\n",

diff --git a/notebooks/Synergistic/HKEM_reconstruction.ipynb b/notebooks/Synergistic/HKEM_reconstruction.ipynb
@@ -67,7 +67,7 @@
    "outputs": [],
    "source": [
     "#%% make sure figures appears inline and animations works\n",
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "\n",
     "# Setup the working directory for the notebook\n",
     "import notebook_setup\n",

diff --git a/notebooks/Synergistic/MAPEM_Bowsher.ipynb b/notebooks/Synergistic/MAPEM_Bowsher.ipynb
@@ -57,7 +57,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "\n",
     "# Setup the working directory for the notebook\n",
     "import notebook_setup\n",

diff --git a/notebooks/Synergistic/Solutions/Dual_PET_Answer-noMotion.ipynb b/notebooks/Synergistic/Solutions/Dual_PET_Answer-noMotion.ipynb
@@ -55,7 +55,7 @@
     "# plotting settings\n",
     "plt.ion() # interactive 'on' such that plots appear during loops\n",
     "\n",
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "\n",
     "#%% some handy function definitions\n",
     "def imshow(image, limits=None, title=''):\n",

diff --git a/notebooks/Synergistic/Solutions/Dual_PET_Answer-wMotion.ipynb b/notebooks/Synergistic/Solutions/Dual_PET_Answer-wMotion.ipynb
@@ -54,7 +54,7 @@
     "# plotting settings\n",
     "plt.ion() # interactive 'on' such that plots appear during loops\n",
     "\n",
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "\n",
     "#%% some handy function definitions\n",
     "def imshow(image, limits=None, title=''):\n",

diff --git a/notebooks/Synergistic/cil_joint_tv_PET.ipynb b/notebooks/Synergistic/cil_joint_tv_PET.ipynb
@@ -47,7 +47,7 @@
    "outputs": [],
    "source": [
     "# Make sure figures appears inline\n",
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "%matplotlib inline"
    ]
   },

diff --git a/notebooks/Synergistic/cil_joint_tv_PET_SPECT.ipynb b/notebooks/Synergistic/cil_joint_tv_PET_SPECT.ipynb
@@ -47,7 +47,7 @@
    "outputs": [],
    "source": [
     "# Make sure figures appears inline\n",
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "%matplotlib inline"
    ]
   },

diff --git a/notebooks/Synergistic/cil_joint_tv_mr.ipynb b/notebooks/Synergistic/cil_joint_tv_mr.ipynb
@@ -45,7 +45,7 @@
    "outputs": [],
    "source": [
     "# Make sure figures appears inline and animations works\n",
-    "%matplotlib notebook"
+    "%matplotlib widget"
    ]
   },
   {

diff --git a/notebooks/Synergistic/gradient_descent_mr_pet_ct.ipynb b/notebooks/Synergistic/gradient_descent_mr_pet_ct.ipynb
@@ -48,7 +48,7 @@
    "outputs": [],
    "source": [
     "# Make sure figures appears inline and animations works\n",
-    "%matplotlib notebook\n",
+    "%matplotlib widget\n",
     "\n",
     "# Setup the working directory for the notebook\n",
     "import notebook_setup\n",