clearer name for the channel in which a spot is detected

gerlichlab · Oct 12, 2024 · 60d7288 · 60d7288
1 parent 16745ff
commit 60d7288
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Showing 5 changed files with 8 additions and 25 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 * `Area` and `MeanIntensity` data types, in a new subpackage--`measurement`--of the `roi` module.
+* Many new data types and typeclass instances.
 
 ## [v0.1.0] - 2024-07-10
 

diff --git a/modules/io/src/main/scala/csv/Columns.scala b/modules/io/src/main/scala/csv/Columns.scala
@@ -54,7 +54,7 @@ object ColumnNames:
   val TimepointColumnName = ColumnName[ImagingTimepoint]("timepoint")
 
   /** Key for field of imaging channel */
-  val ChannelColumnName = ColumnName[ImagingChannel]("roiChannel")
+  val SpotChannelColumnName = ColumnName[ImagingChannel]("spotChannel")
 
   /** Key for z-coordinate of spot centroid */
   def zCenterColumnName[C] = ColumnName[ZCoordinate[C]]("zc")

diff --git a/modules/io/src/main/scala/csv/instances/InstancesForImaging.scala b/modules/io/src/main/scala/csv/instances/InstancesForImaging.scala
@@ -56,31 +56,13 @@ trait InstancesForImaging:
   given CellEncoder[ImagingTimepoint] =
     CellEncoder.fromSimpleShow[ImagingTimepoint]
 
-  given defaultCsvRowDecoderForImagingContext(using
-      CellDecoder[FieldOfViewLike],
-      CellDecoder[ImagingTimepoint],
-      CellDecoder[ImagingChannel]
-  ): CsvRowDecoder[ImagingContext, String] = new:
-    override def apply(row: RowF[Some, String]): DecoderResult[ImagingContext] =
-      val fovNel = ColumnNames.FieldOfViewColumnName.from(row)
-      val timeNel = ColumnNames.TimepointColumnName.from(row)
-      val channelNel = ColumnNames.ChannelColumnName.from(row)
-      (fovNel, timeNel, channelNel)
-        .mapN(ImagingContext.apply)
-        .toEither
-        .leftMap { messages =>
-          DecoderError(
-            s"Cannot decode imaging context because of ${messages.length} error(s): ${messages.mkString_("; ")}"
-          )
-        }
-
   given csvRowEncoderForImagingContext(using
       encFov: CellEncoder[FieldOfViewLike],
       envTime: CellEncoder[ImagingTimepoint],
-      encChannel: CellEncoder[ImagingChannel]
+      encChannel: CsvRowEncoder[ImagingChannel, String]
   ): CsvRowEncoder[ImagingContext, String] = new:
     override def apply(elem: ImagingContext): RowF[Some, String] =
       val fovRow = ColumnNames.FieldOfViewColumnName.write(elem.fieldOfView)
       val timeRow = ColumnNames.TimepointColumnName.write(elem.timepoint)
-      val channelRow = ColumnNames.ChannelColumnName.write(elem.channel)
+      val channelRow = encChannel(elem.channel)
       fovRow |+| timeRow |+| channelRow
diff --git a/modules/io/src/main/scala/csv/instances/InstancesForRoi.scala b/modules/io/src/main/scala/csv/instances/InstancesForRoi.scala
@@ -93,7 +93,7 @@ trait InstancesForRoi:
   def getCsvRowDecoderForDetectedSpot[C](
       fovCol: ColumnNameLike[FieldOfViewLike] = FieldOfViewColumnName,
       timeCol: ColumnNameLike[ImagingTimepoint] = TimepointColumnName,
-      channelCol: ColumnNameLike[ImagingChannel] = ChannelColumnName,
+      channelCol: ColumnNameLike[ImagingChannel] = SpotChannelColumnName,
       zCol: ColumnNameLike[ZCoordinate[C]] = zCenterColumnName[C],
       yCol: ColumnNameLike[YCoordinate[C]] = yCenterColumnName[C],
       xCol: ColumnNameLike[XCoordinate[C]] = xCenterColumnName[C],
@@ -136,7 +136,7 @@ trait InstancesForRoi:
   def getCsvRowEncoderForDetectedSpot[C](
       fovCol: ColumnNameLike[FieldOfViewLike] = FieldOfViewColumnName,
       timeCol: ColumnNameLike[ImagingTimepoint] = TimepointColumnName,
-      channelCol: ColumnNameLike[ImagingChannel] = ChannelColumnName,
+      channelCol: ColumnNameLike[ImagingChannel] = SpotChannelColumnName,
       zCol: ColumnNameLike[ZCoordinate[C]] = zCenterColumnName[C],
       yCol: ColumnNameLike[YCoordinate[C]] = yCenterColumnName[C],
       xCol: ColumnNameLike[XCoordinate[C]] = xCenterColumnName[C],

diff --git a/modules/zarr/src/main/scala/OmeZarrDimension.scala b/modules/zarr/src/main/scala/OmeZarrDimension.scala
@@ -160,10 +160,10 @@ object OmeZarr:
           .one(s"Expected 5 dimensions but got ${indexedDims.length}")
           .asLeft
       else
-        val tNel = getUniqueIndexFor("time")(
+        val tNel = getUniqueIndexFor(timeName)(
           _.isInstanceOf[TimepointDimension]
         )(indexedDims).toValidatedNel
-        val cNel = getUniqueIndexFor("channel")(
+        val cNel = getUniqueIndexFor(channelName)(
           _.isInstanceOf[ChannelDimension]
         )(indexedDims).toValidatedNel
         val zNel = getUniqueIndexFor("z")(_.isInstanceOf[ZDimension])(