Tutorial improvements #57

Treiblesschorle · 2018-08-13T15:35:57Z

No description provided.

Fix typos Remove empty cells

imagejan

Just a few minor comments.

imagejan · 2018-08-13T16:04:59Z

notebooks/1_-_Using_ImageJ/1_-_Fundamentals_of_ImageJ.ipynb

@@ -164,7 +164,7 @@
    "\n",
    "<p><img src=\"ide-autocomplete.png\"></p>\n",
    "\n",
-    "Unfortunately, here in this notebook software, the autocompletion logic is not (yet!) advanced enough to fully offer such a feature—there is only rudimentary method completion support by pressing <kbd>tab</kbd>. Hence, the `NotebookService` also includes a handy method for inspecting an object's methods. Here is an example:"
+    "Unfortunately, here in this notebook software, the autocompletion logic is not (yet!) advanced enough to fully offer such a feature—there is only rudimentary method completion support by pressing <kbd>tab</kbd>. Hence, the `NotebookService` also includes a handy method for inspecting an object's methods. Here is an example which will show the vailable ethods of a List:"


s/ethods/methods/

Also s/vailable/available/

imagejan · 2018-08-13T16:06:33Z

notebooks/1_-_Using_ImageJ/ImageJ_Ops/06_-_Evaluating_Expressions.ipynb

@@ -105,7 +105,7 @@
   "source": [
    "You can also call any op in an `eval` statement as a function, using familiar function syntax.\n",
    "\n",
-    "Here is an example of the `eval` op being used to compute a [Difference of Gaussians](https://en.wikipedia.org/wiki/Difference_of_Gaussians):"
+    "The following is an example of the `eval` op being used to compute a [Difference of Gaussians](https://en.wikipedia.org/wiki/Difference_of_Gaussians). Inputs within the formula may be accessed via the `Map vars?` argument of the eval function. Thereby, the key of the map corresponds to the name of the variable that can be used in the formula."


Wrong use of "thereby", no?

"In which" might be a good substitute for the "thereby"

imagejan · 2018-08-13T16:08:53Z

notebooks/1_-_Using_ImageJ/ImageJ_Ops/13_-_Frangi_Vesselness_Filter.ipynb

@@ -77,15 +77,19 @@
    "\n",
    "//scales refers the the pixel distance at which the filter operates. Larger scales measure larger structures.\n",
    "//spacing refers to the physical distance between pixels. The default setting is {1, 1, 1...}\n",
-    "#@String(label=\"spacing: e.g. \\\"1, 1, 1\\\"\",value=\"1, 1, 1\") spacing\n",
+    "spacings = [1.0, 1.0, 1.0]\n",


Why did you remove the script parameters?

It was not used in the example. For the sake of the example its easier to just use a list. Also, then one can remove the parsing of the input String into a list.

gselzer

For the most part looks good! I just had a few wording suggestions, but after that looks good by me!

gselzer · 2018-08-20T14:09:42Z

notebooks/1_-_Using_ImageJ/1_-_Fundamentals_of_ImageJ.ipynb

@@ -164,7 +164,7 @@
    "\n",
    "<p><img src=\"ide-autocomplete.png\"></p>\n",
    "\n",
-    "Unfortunately, here in this notebook software, the autocompletion logic is not (yet!) advanced enough to fully offer such a feature—there is only rudimentary method completion support by pressing <kbd>tab</kbd>. Hence, the `NotebookService` also includes a handy method for inspecting an object's methods. Here is an example:"
+    "Unfortunately, here in this notebook software, the autocompletion logic is not (yet!) advanced enough to fully offer such a feature—there is only rudimentary method completion support by pressing <kbd>tab</kbd>. Hence, the `NotebookService` also includes a handy method for inspecting an object's methods. Here is an example which will show the vailable ethods of a List:"


Also s/vailable/available/

gselzer · 2018-08-20T14:20:37Z

notebooks/1_-_Using_ImageJ/1_-_Fundamentals_of_ImageJ.ipynb

@@ -656,7 +657,7 @@
   "cell_type": "markdown",
   "metadata": {},
   "source": [
-    "The true meat of ImageJ is [ImageJ Ops](https://imagej.net/Ops), a library for reusable image processing. An `Op` plugin is form of `Command`, and therefore a module.\n",
+    "The true meat of ImageJ is [ImageJ Ops](https://imagej.net/Ops), a library for reusable image processing. An `Op` plugin is a form of `Command`, and therefore a module.\n",


Seeing as we have not yet explained what a Command is maybe we should say something along the lines of "An Op is a special type of Module called a Command (see "Modules"\ below).

gselzer · 2018-08-20T14:25:22Z

notebooks/1_-_Using_ImageJ/ImageJ_Ops/06_-_Evaluating_Expressions.ipynb

@@ -105,7 +105,7 @@
   "source": [
    "You can also call any op in an `eval` statement as a function, using familiar function syntax.\n",
    "\n",
-    "Here is an example of the `eval` op being used to compute a [Difference of Gaussians](https://en.wikipedia.org/wiki/Difference_of_Gaussians):"
+    "The following is an example of the `eval` op being used to compute a [Difference of Gaussians](https://en.wikipedia.org/wiki/Difference_of_Gaussians). Inputs within the formula may be accessed via the `Map vars?` argument of the eval function. Thereby, the key of the map corresponds to the name of the variable that can be used in the formula."


"In which" might be a good substitute for the "thereby"

gselzer · 2018-08-20T14:33:21Z

notebooks/1_-_Using_ImageJ/ImageJ_Ops/03_-_Generating_Images.ipynb

@@ -230,7 +230,8 @@
   "source": [
    "The `equation` op allows you to generate an image from a formula in JavaScript syntax.\n",
    "\n",
-    "Such images can be useful for testing without needing an external image source, or a long and bulky list of numbers."
+    "Such images can be useful for testing without needing an external image source, or a long and bulky list of numbers.\n",
+    "Thereby the equation will be executed on each pixel of the image. Within the equation the current location can be retrieved via the variable `p[]` (see example equation below)."


The thereby here is also a little strange. Maybe "This Op will execute the equation on each pixel of the image" is a better sentence?

gselzer · 2018-08-20T14:56:58Z

notebooks/3_-_Advanced_usage/2_-_Under_the_hood_-_ImgLib2.ipynb

-    ">Both, [RandomAccess](http://javadoc.imagej.net/ImgLib2/net/imglib2/RandomAccess.html) and [Cursor](http://javadoc.imagej.net/ImgLib2/net/imglib2/Cursor.html) implement the [Sampler](http://javadoc.imagej.net/ImgLib2/net/imglib2/Sampler.html) interface which allows to access pixel values. Both implement the [Localizable](http://javadoc.imagej.net/ImgLib2/net/imglib2/Localizable.html) interface which allows to retrieve the accessors current >pixel coordinates. Both inherit (through Localizable) the [EuclideanSpace](http://javadoc.imagej.net/ImgLib2/net/imglib2/EuclideanSpace.html) interval which allows to get the number of dimensions of the image.\n",
-    "\n",
-    ">Note, that [Sampler](http://javadoc.imagej.net/ImgLib2/net/imglib2/Sampler.html), [RandomAccess](http://javadoc.imagej.net/ImgLib2/net/imglib2/RandomAccess.html), and [Cursor](http://javadoc.imagej.net/ImgLib2/net/imglib2/Cursor.html) have a type paramer **< T >** that refers to the value type of the underlying image."
+    ">Both, [RandomAccess](http://javadoc.imagej.net/ImgLib2/net/imglib2/RandomAccess.html) and [Cursor](http://javadoc.imagej.net/ImgLib2/net/imglib2/Cursor.html) implement the [Sampler](http://javadoc.imagej.net/ImgLib2/net/imglib2/Sampler.html) interface which allows to access pixel values. Both implement the [Localizable](http://javadoc.imagej.net/ImgLib2/net/imglib2/Localizable.html) interface which allows to retrieve the accessors current >pixel coordinates. Both inherit (through Localizable) the [EuclideanSpace](http://javadoc.imagej.net/ImgLib2/net/imglib2/EuclideanSpace.html) interval which allows to get the number of dimensions of the image.    \n",


The comma after the Both is wrong, no?

gselzer · 2018-08-20T15:05:16Z

notebooks/1_-_Using_ImageJ/ImageJ_Ops/13_-_Frangi_Vesselness_Filter.ipynb

+    "shape = new HyperSphereShape(1)\n",
+    "dilate = ij.op().morphology().dilate(actualOutput, shape)\n",
+    "\n",
+    "[[\"Output: \":actualOutput, \"Dilated: \":dilate]]"


Do we really want to use an Op in a notebook dedicated to a different Op?

Honestly I am not sure that it is worth fixing this notebook. There already exists a Frangi Vesselness notebook in the new Ops scheme (one notebook for every Op), so this notebook will probably be deleted later on.

DaveK-KNIME added 4 commits August 10, 2018 23:51

Add further explanations

4caba14

Fix typos Remove empty cells

Remove unused code

8dd902e

Rephrase

aa8a6e9

Add some code to better show the outputs

28e4ce7

Treiblesschorle requested a review from ctrueden August 13, 2018 15:35

imagejan reviewed Aug 13, 2018

View reviewed changes

Fix typos

0152516

Treiblesschorle requested a review from gselzer August 17, 2018 16:47

gselzer reviewed Aug 20, 2018

View reviewed changes

ctrueden added the to do label Oct 3, 2018

ctrueden self-assigned this Oct 3, 2018

ctrueden closed this in c787644 Feb 25, 2019

ctrueden deleted the tutorial_improvements branch February 25, 2019 21:38

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Tutorial improvements #57

Tutorial improvements #57

Treiblesschorle commented Aug 13, 2018

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Tutorial improvements #57

Tutorial improvements #57

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