Merge branch 'polish-docs'

ctrueden · ctrueden · commit 856115a6fed4 · 2024-06-03T20:47:28.000-05:00
Fix a few small issues in the documentation.
diff --git a/docs/ops/doc/CallingOps.md b/docs/ops/doc/CallingOps.md
@@ -72,15 +72,31 @@ direct execution, since the parameters have not been concretely specified yet.
 Using [wildcards](https://docs.oracle.com/javase/tutorial/extra/generics/wildcards.html), such as `Img<?> inImage`, can make Op reuse difficult. For example, the following code segment will not compile in a Java runtime:
 
 ```java
-Img<?> inImage = ...;
+Img<?> inImage = ArrayImgs.unsignedBytes(128, 128);
 var gaussOp = ops.op("filter.gauss").input(inImage, 2.0).output(outImage).computer();
 gaussOp.compute(inImage, 2.0, outImage);
 ```
 
 ### Solution 1: Use `compute` instead of `computer`
 
-If you don't need to save the Op to a variable, *just call it directly* as shown [here](#computing-with-compute). Generally speaking, op requests are **cached**, meaning repeated OpBuilder calls that directly execute Ops will **not** significantly increase performance.
+If you don't need to save the Op to a variable, *just [call it directly](#computing-with-compute)*:
 
-### Solution 2: Use Type Parameters on your functions
+```java
+ops.op("filter.gauss").input(inImage, 2.0).output(outImage).compute();
+```
+
+Generally speaking, op requests are **cached**, meaning repeated OpBuilder calls that directly execute Ops will **not** significantly decrease performance.
+
+### Solution 2: Avoid using wildcards
+
+If you *know* that your `Img` will always contain unsigned byte values, for example, define your variable as an `Img<UnsignedByteType>` rather than using `Img<?>`.
+
+### Solution 3: Use raw casts (not type-safe!)
+
+```java
+Img<?> inImage = ArrayImgs.unsignedBytes(128, 128);
+var gaussOp = ops.op("filter.gauss").input(inImage, 2.0).output(outImage).computer();
+gaussOp.compute((Img) inImage, 2.0, outImage);
+```
 
-If you *know* that your `Img` will always contain bytes, define your variable as an `Img<ByteType>`
+This method should only be used as a last resort.
diff --git a/docs/ops/doc/examples/flim_analysis.rst b/docs/ops/doc/examples/flim_analysis.rst
@@ -13,7 +13,7 @@ We use a sample of `FluoCells™ Prepared Slide #1`_, imaged by `Jenu Chacko`_ u
 
   FluoCells™ Prepared Slide #1 contains bovine pulmonary artery endothelial cells (BPAEC). MitoTracker™ Red CMXRos was used to stain the mitochondria in the live cells, with accumulation dependent upon membrane potential. Following fixation and permeabilization, F-actin was stained with Alexa Fluor™ 488 phalloidin, and the nuclei were counterstained with the blue-fluorescent DNA stain DAPI.
 
-The sample data can be downloaded `here <https://media.scijava.org/scijava-ops/1.0.0/flim_example_data.sdt>`_ and can be loaded into Fiji with `Bio-Formats`_ using ``File → Open``. When presented with the ``Bio-Formats Import Options`` screen, it may be helpful to select ``Metadata viewing → Display metadata`` to determine values necessary for analysis. Then, select ``OK``. The data may take a minute to load.
+The sample data can be downloaded `here <https://media.scijava.org/scijava-ops/1.0.0/flim_example_data.sdt>`_ and can be loaded into Fiji with `SCIFIO`_ using ``File → Open...`` or ``File → Import → Image...``. The data may take a minute to load.
 
 Within the script, the `Levenberg-Marquardt algorithm`_ fitting Op of SciJava Ops FLIM is used to fit the data.
 
@@ -78,7 +78,7 @@ The pseudocolored result shows a clear separation of fluorophores, which could b
         #@ ROIService roiService
         #@ Img input
         #@ Float (description="The total time (ns) (timeBase in metadata)", label = "Time Base", value=12.5) timeBase
-        #@ Integer (description="The number of time bins (timeBins in metadata)", label = "Time Bins", value=512) timeBins
+        #@ Integer (description="The number of time bins (timeBins in metadata)", label = "Time Bins", value=256) timeBins
         #@ Integer (description="The index of the lifetime axis (from metadata)", label = "Lifetime Axis", value=2) lifetimeAxis
         #@ Float (description="The minimal pixel intensity (across all time bins) threshold for fitting", label = "Intensity Threshold", value = 18) iThresh
         #@ Integer (description="The radius of the binning kernel", label = "Bin Kernel Radius", value=1, min=0) kernelRad
@@ -222,7 +222,7 @@ In the panels below, we show the results of executing both scripts with computat
     :width: 49%
 
 
-.. _`Bio-Formats` : https://www.openmicroscopy.org/bio-formats/
+.. _`SCIFIO` : https://scif.io
 .. _`FLIM` : https://en.wikipedia.org/wiki/Fluorescence-lifetime_imaging_microscopy
 .. _`FluoCells™ Prepared Slide #1` : https://www.thermofisher.com/order/catalog/product/F36924
 .. _`FRET` : https://en.wikipedia.org/wiki/F%C3%B6rster_resonance_energy_transfer
diff --git a/docs/ops/doc/examples/gaussian_subtraction.rst b/docs/ops/doc/examples/gaussian_subtraction.rst
@@ -1,11 +1,11 @@
 =========================
-Gaussian blur subtraction
+Gaussian Blur Subtraction
 =========================
 
-In this example we will use SciJava Ops to open an image, apply a guassian blur and subract the blurred image from the input image.
+In this example we will use SciJava Ops to open an image, apply a gaussian blur and subtract the blurred image from the input image.
 This technique can be used to extract features, such as puncta, from a noisy background.
 
-SciJava Ops via Fiji's sripting engine with `script parameters`_:
+Here is a script using `script parameters`_, runnable in Fiji's `Script Editor`_:
 
 .. tabs::
 
@@ -53,4 +53,5 @@ SciJava Ops via Fiji's sripting engine with `script parameters`_:
         result = ops.op("create.img").input(img, FloatType()).apply()
         ops.op("math.sub").input(img, img_gauss).output(result).compute()
 
-.. _`script parameters`: https://imagej.net/scripting/parameters 
+.. _`script parameters`: https://imagej.net/scripting/parameters
+.. _`Script Editor`: https://imagej.net/scripting/script-editor
diff --git a/docs/ops/doc/examples/saca.rst b/docs/ops/doc/examples/saca.rst
@@ -169,5 +169,5 @@ To apply the ``phase`` LUT and a colorbar use the following script and select th
 .. _`Becker and Sherer, JVI 2017`: https://pubmed.ncbi.nlm.nih.gov/28053097/
 .. _`Wang et. al, IEEE 2019`: https://ieeexplore.ieee.org/abstract/document/8681436
 .. _`Stockley et. al, Bacteriophage 2016`: https://pubmed.ncbi.nlm.nih.gov/27144089/
-.. _`here`: https://media.imagej.net/scijava-ops/1.0.0/hela_hiv_gag_ms2_mcherry.tif
+.. _`here`: https://media.scijava.org/scijava-ops/1.0.0/hela_hiv_gag_ms2_mcherry.tif
 .. _`script parameters`: https://imagej.net/scripting/parameters
diff --git a/scijava-ops-engine/src/main/java/module-info.java b/scijava-ops-engine/src/main/java/module-info.java
@@ -43,10 +43,11 @@
 	requires org.scijava.priority;
 	requires org.scijava.progress;
 	requires org.scijava.struct;
-	requires transitive org.scijava.ops.api;
+	requires org.scijava.ops.api;
 	requires org.scijava.ops.spi;
 	requires org.scijava.types;
 
+	requires com.google.common;
 	requires org.javassist;
 	requires org.slf4j;
 	requires org.yaml.snakeyaml;
diff --git a/scijava-ops-engine/templates/main/java/module-info.vm b/scijava-ops-engine/templates/main/java/module-info.vm
@@ -15,10 +15,11 @@ module org.scijava.ops.engine {
 	requires org.scijava.priority;
 	requires org.scijava.progress;
 	requires org.scijava.struct;
-	requires transitive org.scijava.ops.api;
+	requires org.scijava.ops.api;
 	requires org.scijava.ops.spi;
 	requires org.scijava.types;
 
+	requires com.google.common;
 	requires org.javassist;
 	requires org.slf4j;
 	requires org.yaml.snakeyaml;
