Merge pull request #1 from din14970/review

Review

210910AdvancedIndexing.ipynb

@@ -77,7 +77,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 5,
    "id": "6df5fe6c",
    "metadata": {},
    "outputs": [
@@ -155,7 +155,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 6,
    "id": "b71ce71c",
    "metadata": {},
    "outputs": [
@@ -165,7 +165,7 @@
        "<LazyElectronDiffraction2D, title: , dimensions: (260, 200|256, 256)>"
       ]
      },
-     "execution_count": 4,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -184,7 +184,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 7,
    "id": "e18ad0dd",
    "metadata": {},
    "outputs": [
@@ -219,17 +219,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 8,
    "id": "377320d2",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "<matplotlib.image.AxesImage at 0x7f993c227dc0>"
+       "<matplotlib.image.AxesImage at 0x7f64a899bd30>"
       ]
      },
-     "execution_count": 6,
+     "execution_count": 8,
      "metadata": {},
      "output_type": "execute_result"
     },
@@ -285,7 +285,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 3,
    "id": "5571e021",
    "metadata": {},
    "outputs": [
@@ -327,7 +327,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 4,
    "id": "6fc6f95c",
    "metadata": {},
    "outputs": [
@@ -974,7 +974,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 29,
+   "execution_count": 9,
    "id": "627396ab",
    "metadata": {},
    "outputs": [
@@ -3918,14 +3918,6 @@
    "source": [
     "fig.savefig(\"210903DataImages/210921AnalysisG.png\", dpi=640)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "4ad6ef42",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {

Dockerfile

@@ -42,19 +42,19 @@ RUN conda init bash && \
                                  matplotlib-scalebar=0.7.2 \
                                  scikit-learn=0.24.2 \
                                  lmfit=1.0.2 \
-                                 numpy=1.21.2 \
-                                 numba=0.53.1 \
+                                 numpy=1.20.3 \
+                                 numba=0.55.1 \
                                  psutil=5.8.0 \
                                  ipywidgets=7.6.5 \
                                  ipyevents=2.0.1 \
                                  scipy=1.7.1 \
                                  diffpy.structure=3.0.1 \
                                  tqdm=4.62.2 \
                                  transforms3d=0.3.1 \
-                                 orix=0.7.0 \
-                                 dask=2021.7.1 \
+                                 orix=0.8.2 \
+                                 dask=2021.9.1 \
                                  h5py=3.3.0 \
-                                 hyperspy=1.6.4 \
+                                 hyperspy=1.6.5 \
                                  pywget=3.2 \
                                  vtk=9.0.3
 
@@ -66,12 +66,12 @@ RUN conda init bash && . /root/.bashrc && conda activate venv && \
 
 # installing the custom packages
 RUN conda init bash && . /root/.bashrc && conda activate venv && \
-    git clone https://github.com/din14970/diffsims.git \
-    && cd diffsims && git checkout 29b0715 && pip install -e .
+    git clone https://github.com/pyxem/diffsims.git \
+    && cd diffsims && git checkout 2b75329 && pip install -e .
 
 RUN conda init bash && . /root/.bashrc && conda activate venv && \
     git clone https://github.com/pyxem/pyxem.git \
-    && cd pyxem && git checkout ca4f58de && pip install -e .
+    && cd pyxem && git checkout 30ddc1f5 && pip install -e .
 
 # Add Tini
 ENV TINI_VERSION v0.19.0

README.md

@@ -72,7 +72,7 @@ In order to save you some time I have already included an `environment.yml` file
 
 5. Go out of this folder and clone the repositories for pyxem and diffsims 
     ```
-    $ git clone https://github.com/din14970/diffsims.git
+    $ git clone https://github.com/pyxem/diffsims.git
     ```
 
     and 
@@ -85,19 +85,19 @@ In order to save you some time I have already included an `environment.yml` file
     ```
     $ conda activate pyxenv
     $ cd diffsims
-    $ git checkout 29b0715
+    $ git checkout 2b75329 
     $ python3 -m pip install -e .
     $ cd ../pyxem
-    $ git checkout ca4f58de
+    $ git checkout 30ddc1f5
     $ python3 -m pip install -e .
     ```
     These steps are necessary because the notebooks use specific features which have not yet been packaged into an official version of the software.
 
 7. You should now be able to launch a Jupyter notebook server with `$ jupyter notebook` and open and run the notebooks. Always ensure the virtual environment is active.
 
 If you want GPU acceleration to work you will need to also install `cupy` with a version >9.0.0.
-Additionally you may have to install the appropriate NVIDIA drivers.
+Additionally you may have to install the appropriate NVIDIA drivers and the cuda toolkit.
 If you can import `cupy` in a notebook and create an array with `cupy.array([1, 2, 3])` without errors, the GPU acceleration should work.
 
 If Mayavi doesn't work on your system you may have to do some digging on required system packages.
-Pyxem does not rely on Mayavi, only one image uses this package.
+Pyxem does not rely on Mayavi, only one image from the paper relies on this package.

data/timings_py4dstem.csv

@@ -0,0 +1,10 @@
+,deltaz,s,deltaphi,mean,std,N
+0,3.0,16,5.0,0.004885721206665039,0.0002752652265211118,190
+1,3.0,16,1.0,0.02255721092224121,9.152533697429926e-05,190
+2,3.0,16,0.2,0.11132421493530273,0.0004213860337622292,190
+3,1.0,16,5.0,0.046873044967651364,0.00022924351924179484,1596
+4,1.0,16,1.0,0.18623886108398438,0.001506090134745518,1596
+5,1.0,16,0.2,0.9322866439819336,0.009127655975065572,1596
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+7,0.5,16,1.0,0.7188356399536133,0.0024698227241183018,6105
+8,0.5,16,0.2,4.888544130325317,2.645356733933859,6105

environment.yml

@@ -11,19 +11,19 @@ dependencies:
   - matplotlib-scalebar=0.7.2
   - scikit-learn=0.24.2
   - lmfit=1.0.2
-  - numpy=1.21.2
-  - numba=0.53.1
+  - numpy=1.20.3
+  - numba=0.55.1
   - psutil=5.8.0
   - ipywidgets=7.6.5
   - ipyevents=2.0.1
   - scipy=1.7.1
   - diffpy.structure=3.0.1
   - tqdm=4.62.2
   - transforms3d=0.3.1
-  - orix=0.7.0
-  - dask=2021.7.1
+  - orix=0.8.2
+  - dask=2021.9.1
   - h5py=3.3.0
-  - hyperspy=1.6.4
+  - hyperspy=1.6.5
   - pywget=3.2
   - vtk=9.0.3
   - mayavi=4.7.2

pyxem_cpu_time.csv

@@ -0,0 +1,97 @@
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