micro-reader 0.0.2__tar.gz → 0.0.4__tar.gz

{micro_reader-0.0.2 → micro_reader-0.0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: micro-reader
-Version: 0.0.2
+Version: 0.0.4
 Summary: Low-level, memory-bounded pixel reading for microscopy formats: read exactly the rectangle you ask for.
 Project-URL: Homepage, https://github.com/bugraoezdemir/micro-reader
 Project-URL: Source, https://github.com/bugraoezdemir/micro-reader
@@ -54,7 +54,7 @@ Description-Content-Type: text/markdown
 
 **Memory-bounded pixel reader for microscopy images.**
 
-`micro-reader` reads regions of large microscopy files without loading the entire image into memory. It provides a common interface across TIFF, CZI, ND2, Leica, OIR, Imaris, MRC, and common raster formats.
+`micro-reader` reads regions of large microscopy files without loading the entire image into memory. It provides a common interface across TIFF, CZI, ND2, Leica, OIR, OIB / OIF, Olympus VSI, Imaris, DeltaVision, MRC, common raster formats, OME companion file sets, and high-content screening plates (Harmony, MetaXpress, IN Cell, CellVoyager).
 
 > **Status: pre-alpha (0.0.x)**
 >
@@ -192,6 +192,10 @@ This returns the images matching the requested indices. For example, if a file c
 `micro-reader` uses these index names when a format provides the corresponding dimensions:
 
 ```text
+plate
+acquisition
+well
+field
 scene
 tile
 rotation
@@ -203,11 +207,37 @@ emission
 excitation
 lifetime
 sequence
+part
 resolution
 ```
 
 Only dimensions actually present in a file appear in an image's index.
 
+### Files made of several files
+
+Some formats always come as several files: an OIR file with its continuation files (`name_00001`), a Micro-Manager stack split over `..._MMStack_Pos0.ome.tif`, `..._MMStack_Pos0_1.ome.tif`, an NDTiff folder, an Olympus OIF with its `.oif.files` folder, an Olympus VSI with its `_name_` folder, a DeltaVision image with its softWoRx `.log`, a plate's side files (Harmony `Assaylayout/` and `FFC_Profile/`, CellVoyager settings files, MetaXpress `_thumb` previews). Opening any of these files opens the whole image:
+
+```python
+f = micro_reader.open("cells_R3D.dv.log")
+f.path     # the main file: "cells_R3D.dv"
+f.opened   # what was opened: "cells_R3D.dv.log"
+```
+
+You can also open the folder. A folder opens the image it belongs to (an NDTiff dataset folder, a Harmony or CellVoyager measurement folder), or the one image it holds. A folder with several images raises an error that lists them.
+
+To sort many files at once, for example everything under a folder you want to convert, `group_files` says which files make one image:
+
+```python
+g = micro_reader.group_files("experiment/")
+for group in g.groups:
+    group.main      # the file to open: "slide.vsi", "plate/Index.idx.xml"
+    group.parts     # the other files of a multi-file image
+    group.members   # for a plate or companion index: the files its images come from
+g.singles           # every other file, as given
+```
+
+A file that a plate or companion index names is listed only in that index's group. When the main file of a multi-file image is missing, its group has `main=None`.
+
 ## Axes
 
 An image array uses these axes:
@@ -401,7 +431,7 @@ img_scene0_level2 = f.select(scene=0, resolution=2)[0]
 Supported pyramids include:
 
 * **Imaris**: all stored levels
-* **TIFF**: OME-TIFF and other TIFF pyramids such as SVS and NDPI
+* **TIFF**: OME-TIFF and whole-slide pyramids (SVS, NDPI, SCN, BIF, QPTIFF, Philips)
 * **CZI**: stored pyramids of whole scenes
 
 Other formats expose a single resolution level.
@@ -425,6 +455,43 @@ The tiles are composed according to the format's stitching information.
 
 Currently, stitching is supported for **CZI only**.
 
+## Plates
+
+High-content screening plates are opened through their index file, for example `Index.idx.xml` for Harmony. Each field is one image, indexed by `plate`, `acquisition`, `well` and `field`.
+
+The plate layout is available through:
+
+```python
+plate = f.plates[0]
+plate.wells[0].name
+# "B2"
+```
+
+Images can be reached through the wells, or selected by well:
+
+```python
+image = plate.wells[0].fields[0].image
+f.select(well=plate.well_index("B2"))
+```
+
+`f.outline()` shows the plates, wells and fields of a file.
+
+Zeiss CZI plates are read as plates with `plates=True`, and as scenes otherwise:
+
+```python
+f = micro_reader.open("plate.czi", plates=True)
+```
+
+Missing plane files are read as zeros, with a `MissingImagesWarning`. A field without any of its files is left out.
+
+A plane file whose size or pixel type differs from what the index describes raises an error when it is read. To find such files before reading anything, check them all at once:
+
+```python
+f.check_members()   # opens every plane file once; returns how many were checked
+```
+
+When the channels of a field have different z sampling, `image.parts` gives one image per group of channels that share it.
+
 ## Metadata
 
 Pixel and channel metadata are available through:
@@ -488,13 +555,18 @@ The position is omitted when it cannot be determined reliably.
 
 | Format               | Notes                                                 |
 | -------------------- | ----------------------------------------------------- |
-| **TIFF / BigTIFF**   | TIFF, OME-TIFF, ImageJ, LSM, STK and TIFF pyramids    |
+| **TIFF / BigTIFF**   | TIFF, OME-TIFF, ImageJ, LSM, STK, Micro-Manager, whole-slide TIFFs |
+| **OME companion**    | `.companion.ome` sets of OME-TIFF files               |
 | **CZI**              | Zeiss CZI, including mosaic tiles and stitched scenes |
 | **ND2**              | Nikon ND2, including legacy JPEG 2000 ND2             |
 | **Leica**            | LIF, LOF, LIFEXT, XLIF, XLEF, XLCF                    |
 | **OIR**              | Olympus / Evident FluoView                            |
+| **OIB / OIF**        | Olympus FluoView FV1000 / FV1200 / FV3000             |
+| **VSI**              | Olympus / Evident cellSens and VS120 / VS200 slide scanners |
 | **Imaris**           | `.ims`, with the `[ims]` extra                        |
+| **DeltaVision**      | `.dv`, `.r3d` (softWoRx, OMX, Priism)                 |
 | **MRC**              | Common MRC modes and extended headers                 |
+| **Plates (HCS)**     | Harmony, MetaXpress, IN Cell and CellVoyager plates   |
 | **JPEG / PNG / BMP** | Common raster image formats                           |
 
 All formats use the same `File`, `Image`, axes, indexing, metadata, and reading interface wherever possible.
@@ -511,6 +583,14 @@ Supported TIFF formats include:
 * ImageJ
 * Zeiss LSM
 * MetaMorph STK
+* Micro-Manager stacks (MMStack and NDTiff), also when one acquisition is spread over several files
+* Whole-slide TIFFs: Aperio SVS, Hamamatsu NDPI, Leica SCN, Ventana BIF, PerkinElmer / Akoya QPTIFF and Philips
+
+Micro-Manager stage positions are scenes. NDTiff channel names and pixel sizes come from the dataset's index and frame metadata.
+
+A whole-slide file gives the slide first, then the other pictures it stores as further scenes, as Bio-Formats lists them: `label` and `macro` (overview), and for some formats `thumbnail` (QPTIFF) or `probability` (BIF tissue map). Pixel sizes, positions and channel names come from each vendor's own metadata.
+
+Ventana BIF scans store overlapping tiles. They are composed as Roche's description of the format places them. Files from scanners other than the VENTANA DP 200 are not supported.
 
 Compressed TIFF data is decoded only for the strips or tiles needed by the requested region.
 
@@ -534,6 +614,24 @@ Additional codecs such as JPEG XR and LERC are available with:
 pip install "micro-reader[codecs]"
 ```
 
+### OME companion files
+
+An OME companion file (`.companion.ome`) describes images stored in separate TIFF files. Opening the companion reads all those images and groups them together as one `t c z y x` image:
+
+```python
+f = micro_reader.open("data.companion.ome")
+```
+
+Opening one of the TIFF files on its own reads only that file, with its pixel sizes, channels and position taken from the companion. If the companion is missing, the file is read without pixel sizes, with a `CompanionWarning`. A TIFF whose metadata lives in another OME-TIFF (instead of a `.companion.ome`) takes it from that file in the same way.
+
+Some OME-TIFF sets keep the full OME-XML in their TIFF files instead of a companion. Opening one of those files reads the whole set. To read only the planes stored in that file, with the set's metadata:
+
+```python
+f = micro_reader.open("set_t001.ome.tif", multifile=False)
+```
+
+Micro-Manager stacks always open whole, also with `multifile=False`: they split their files by size, so one file does not hold a complete part of the image.
+
 ### CZI
 
 CZI files support:
@@ -595,6 +693,18 @@ These are represented using the common image/index model.
 
 Olympus / Evident FluoView OIR files are supported, including companion files and spectral scans.
 
+### Olympus OIB and OIF
+
+Older FluoView files come in two forms with the same content: an OIB is one file, an OIF is a `.oif` settings file plus a `.oif.files` folder with one TIFF per plane. Both open as one `t c z y x` image, with pixel sizes, z and time steps, channel names, colours and wavelengths. Opening any file in the `.oif.files` folder opens the OIF.
+
+### Olympus VSI
+
+A cellSens VSI is a `.vsi` file plus a `_<name>_` folder that holds the pixels (`stack1/frame_t.ets`, `stack10000/frame_t.ets`, ...). The images are listed as Bio-Formats lists them: one per scanned area, named as in cellSens, with the slide label (`label`) and overview (`overview`) when the scanner took them, and the slide photo (`macro`) last. Each scanned area keeps its resolution levels.
+
+Images are `t c z y x` (`t c z y x s` for brightfield RGB scans), with pixel sizes, z and time steps, and each channel's name, colour and emission wavelength. Stage positions are not read.
+
+Opening the `_<name>_` folder, a `stack` folder or a file in it opens the `.vsi`. An `.ets` file whose `.vsi` is missing is read alone, with a warning, when it is a plain 2-D image; its size is then rounded up to whole tiles.
+
 ### Imaris
 
 Install Imaris support with:
@@ -607,6 +717,12 @@ Imaris resolution level 0 is exposed at the actual image size, with Imaris chunk
 
 Chunked compression is decoded in parallel.
 
+### DeltaVision
+
+DeltaVision files (`.dv`, `.r3d`, `.r3d_d3d`, also deconvolved and projected ones) are recognised by their content, whatever their extension. The image keeps the file's own order of time, waves and z (for example `ctzyx`).
+
+Pixel sizes, and each channel's emission and excitation wavelengths, are read from the file. Channel names come from the softWoRx acquisition log next to it (`<file>.log`); a deconvolved or projected file takes the names from the log of the raw file it was made from. Stage positions are not read.
+
 ### MRC
 
 Supported MRC modes include:

{micro_reader-0.0.2 → micro_reader-0.0.4}/README.md

@@ -2,7 +2,7 @@
 
 **Memory-bounded pixel reader for microscopy images.**
 
-`micro-reader` reads regions of large microscopy files without loading the entire image into memory. It provides a common interface across TIFF, CZI, ND2, Leica, OIR, Imaris, MRC, and common raster formats.
+`micro-reader` reads regions of large microscopy files without loading the entire image into memory. It provides a common interface across TIFF, CZI, ND2, Leica, OIR, OIB / OIF, Olympus VSI, Imaris, DeltaVision, MRC, common raster formats, OME companion file sets, and high-content screening plates (Harmony, MetaXpress, IN Cell, CellVoyager).
 
 > **Status: pre-alpha (0.0.x)**
 >
@@ -140,6 +140,10 @@ This returns the images matching the requested indices. For example, if a file c
 `micro-reader` uses these index names when a format provides the corresponding dimensions:
 
 ```text
+plate
+acquisition
+well
+field
 scene
 tile
 rotation
@@ -151,11 +155,37 @@ emission
 excitation
 lifetime
 sequence
+part
 resolution
 ```
 
 Only dimensions actually present in a file appear in an image's index.
 
+### Files made of several files
+
+Some formats always come as several files: an OIR file with its continuation files (`name_00001`), a Micro-Manager stack split over `..._MMStack_Pos0.ome.tif`, `..._MMStack_Pos0_1.ome.tif`, an NDTiff folder, an Olympus OIF with its `.oif.files` folder, an Olympus VSI with its `_name_` folder, a DeltaVision image with its softWoRx `.log`, a plate's side files (Harmony `Assaylayout/` and `FFC_Profile/`, CellVoyager settings files, MetaXpress `_thumb` previews). Opening any of these files opens the whole image:
+
+```python
+f = micro_reader.open("cells_R3D.dv.log")
+f.path     # the main file: "cells_R3D.dv"
+f.opened   # what was opened: "cells_R3D.dv.log"
+```
+
+You can also open the folder. A folder opens the image it belongs to (an NDTiff dataset folder, a Harmony or CellVoyager measurement folder), or the one image it holds. A folder with several images raises an error that lists them.
+
+To sort many files at once, for example everything under a folder you want to convert, `group_files` says which files make one image:
+
+```python
+g = micro_reader.group_files("experiment/")
+for group in g.groups:
+    group.main      # the file to open: "slide.vsi", "plate/Index.idx.xml"
+    group.parts     # the other files of a multi-file image
+    group.members   # for a plate or companion index: the files its images come from
+g.singles           # every other file, as given
+```
+
+A file that a plate or companion index names is listed only in that index's group. When the main file of a multi-file image is missing, its group has `main=None`.
+
 ## Axes
 
 An image array uses these axes:
@@ -349,7 +379,7 @@ img_scene0_level2 = f.select(scene=0, resolution=2)[0]
 Supported pyramids include:
 
 * **Imaris**: all stored levels
-* **TIFF**: OME-TIFF and other TIFF pyramids such as SVS and NDPI
+* **TIFF**: OME-TIFF and whole-slide pyramids (SVS, NDPI, SCN, BIF, QPTIFF, Philips)
 * **CZI**: stored pyramids of whole scenes
 
 Other formats expose a single resolution level.
@@ -373,6 +403,43 @@ The tiles are composed according to the format's stitching information.
 
 Currently, stitching is supported for **CZI only**.
 
+## Plates
+
+High-content screening plates are opened through their index file, for example `Index.idx.xml` for Harmony. Each field is one image, indexed by `plate`, `acquisition`, `well` and `field`.
+
+The plate layout is available through:
+
+```python
+plate = f.plates[0]
+plate.wells[0].name
+# "B2"
+```
+
+Images can be reached through the wells, or selected by well:
+
+```python
+image = plate.wells[0].fields[0].image
+f.select(well=plate.well_index("B2"))
+```
+
+`f.outline()` shows the plates, wells and fields of a file.
+
+Zeiss CZI plates are read as plates with `plates=True`, and as scenes otherwise:
+
+```python
+f = micro_reader.open("plate.czi", plates=True)
+```
+
+Missing plane files are read as zeros, with a `MissingImagesWarning`. A field without any of its files is left out.
+
+A plane file whose size or pixel type differs from what the index describes raises an error when it is read. To find such files before reading anything, check them all at once:
+
+```python
+f.check_members()   # opens every plane file once; returns how many were checked
+```
+
+When the channels of a field have different z sampling, `image.parts` gives one image per group of channels that share it.
+
 ## Metadata
 
 Pixel and channel metadata are available through:
@@ -436,13 +503,18 @@ The position is omitted when it cannot be determined reliably.
 
 | Format               | Notes                                                 |
 | -------------------- | ----------------------------------------------------- |
-| **TIFF / BigTIFF**   | TIFF, OME-TIFF, ImageJ, LSM, STK and TIFF pyramids    |
+| **TIFF / BigTIFF**   | TIFF, OME-TIFF, ImageJ, LSM, STK, Micro-Manager, whole-slide TIFFs |
+| **OME companion**    | `.companion.ome` sets of OME-TIFF files               |
 | **CZI**              | Zeiss CZI, including mosaic tiles and stitched scenes |
 | **ND2**              | Nikon ND2, including legacy JPEG 2000 ND2             |
 | **Leica**            | LIF, LOF, LIFEXT, XLIF, XLEF, XLCF                    |
 | **OIR**              | Olympus / Evident FluoView                            |
+| **OIB / OIF**        | Olympus FluoView FV1000 / FV1200 / FV3000             |
+| **VSI**              | Olympus / Evident cellSens and VS120 / VS200 slide scanners |
 | **Imaris**           | `.ims`, with the `[ims]` extra                        |
+| **DeltaVision**      | `.dv`, `.r3d` (softWoRx, OMX, Priism)                 |
 | **MRC**              | Common MRC modes and extended headers                 |
+| **Plates (HCS)**     | Harmony, MetaXpress, IN Cell and CellVoyager plates   |
 | **JPEG / PNG / BMP** | Common raster image formats                           |
 
 All formats use the same `File`, `Image`, axes, indexing, metadata, and reading interface wherever possible.
@@ -459,6 +531,14 @@ Supported TIFF formats include:
 * ImageJ
 * Zeiss LSM
 * MetaMorph STK
+* Micro-Manager stacks (MMStack and NDTiff), also when one acquisition is spread over several files
+* Whole-slide TIFFs: Aperio SVS, Hamamatsu NDPI, Leica SCN, Ventana BIF, PerkinElmer / Akoya QPTIFF and Philips
+
+Micro-Manager stage positions are scenes. NDTiff channel names and pixel sizes come from the dataset's index and frame metadata.
+
+A whole-slide file gives the slide first, then the other pictures it stores as further scenes, as Bio-Formats lists them: `label` and `macro` (overview), and for some formats `thumbnail` (QPTIFF) or `probability` (BIF tissue map). Pixel sizes, positions and channel names come from each vendor's own metadata.
+
+Ventana BIF scans store overlapping tiles. They are composed as Roche's description of the format places them. Files from scanners other than the VENTANA DP 200 are not supported.
 
 Compressed TIFF data is decoded only for the strips or tiles needed by the requested region.
 
@@ -482,6 +562,24 @@ Additional codecs such as JPEG XR and LERC are available with:
 pip install "micro-reader[codecs]"
 ```
 
+### OME companion files
+
+An OME companion file (`.companion.ome`) describes images stored in separate TIFF files. Opening the companion reads all those images and groups them together as one `t c z y x` image:
+
+```python
+f = micro_reader.open("data.companion.ome")
+```
+
+Opening one of the TIFF files on its own reads only that file, with its pixel sizes, channels and position taken from the companion. If the companion is missing, the file is read without pixel sizes, with a `CompanionWarning`. A TIFF whose metadata lives in another OME-TIFF (instead of a `.companion.ome`) takes it from that file in the same way.
+
+Some OME-TIFF sets keep the full OME-XML in their TIFF files instead of a companion. Opening one of those files reads the whole set. To read only the planes stored in that file, with the set's metadata:
+
+```python
+f = micro_reader.open("set_t001.ome.tif", multifile=False)
+```
+
+Micro-Manager stacks always open whole, also with `multifile=False`: they split their files by size, so one file does not hold a complete part of the image.
+
 ### CZI
 
 CZI files support:
@@ -543,6 +641,18 @@ These are represented using the common image/index model.
 
 Olympus / Evident FluoView OIR files are supported, including companion files and spectral scans.
 
+### Olympus OIB and OIF
+
+Older FluoView files come in two forms with the same content: an OIB is one file, an OIF is a `.oif` settings file plus a `.oif.files` folder with one TIFF per plane. Both open as one `t c z y x` image, with pixel sizes, z and time steps, channel names, colours and wavelengths. Opening any file in the `.oif.files` folder opens the OIF.
+
+### Olympus VSI
+
+A cellSens VSI is a `.vsi` file plus a `_<name>_` folder that holds the pixels (`stack1/frame_t.ets`, `stack10000/frame_t.ets`, ...). The images are listed as Bio-Formats lists them: one per scanned area, named as in cellSens, with the slide label (`label`) and overview (`overview`) when the scanner took them, and the slide photo (`macro`) last. Each scanned area keeps its resolution levels.
+
+Images are `t c z y x` (`t c z y x s` for brightfield RGB scans), with pixel sizes, z and time steps, and each channel's name, colour and emission wavelength. Stage positions are not read.
+
+Opening the `_<name>_` folder, a `stack` folder or a file in it opens the `.vsi`. An `.ets` file whose `.vsi` is missing is read alone, with a warning, when it is a plain 2-D image; its size is then rounded up to whole tiles.
+
 ### Imaris
 
 Install Imaris support with:
@@ -555,6 +665,12 @@ Imaris resolution level 0 is exposed at the actual image size, with Imaris chunk
 
 Chunked compression is decoded in parallel.
 
+### DeltaVision
+
+DeltaVision files (`.dv`, `.r3d`, `.r3d_d3d`, also deconvolved and projected ones) are recognised by their content, whatever their extension. The image keeps the file's own order of time, waves and z (for example `ctzyx`).
+
+Pixel sizes, and each channel's emission and excitation wavelengths, are read from the file. Channel names come from the softWoRx acquisition log next to it (`<file>.log`); a deconvolved or projected file takes the names from the log of the raw file it was made from. Stage positions are not read.
+
 ### MRC
 
 Supported MRC modes include:

{micro_reader-0.0.2 → micro_reader-0.0.4}/pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "micro-reader"
-version = "0.0.2"
+version = "0.0.4"
 description = "Low-level, memory-bounded pixel reading for microscopy formats: read exactly the rectangle you ask for."
 readme = "README.md"
 requires-python = ">=3.11"

{micro_reader-0.0.2 → micro_reader-0.0.4}/src/micro_reader/__init__.py

@@ -4,22 +4,26 @@
 >>> with micro_reader.open("image.mrc") as f:
 ...     block = f.images[0].read(z=0, y=slice(0, 512))
 """
-from ._base import INDEX_NAMES, SAMPLED_INDICES, File, Image, ReadStats
+from ._base import INDEX_NAMES, PLATE_INDICES, SAMPLED_INDICES, File, Image, ReadStats
 from ._metadata import Channel, Metadata, Quantity
-from ._errors import CorruptFileError, MicroReaderError, UnsupportedFormatError
+from ._plate import Acquisition, Field, Plate, Well
+from ._errors import (CompanionWarning, CompositeWarning, CorruptFileError, MicroReaderError,
+                      MissingImagesWarning, UnsupportedFormatError)
 from ._memory import MemoryLimitError, memory_limit, set_memory_limit
 from ._io import cache_limit, cached_bytes, set_cache_limit
 from ._pool import decode_threads, set_decode_threads
 from ._registry import BACKENDS, open  # noqa: A004 - the public entry point
+from ._groups import FileGroup, Grouping, group_files
 from .backends.czi import DamagedFileWarning
 
-__version__ = "0.0.1"
+__version__ = "0.0.4"
 
 __all__ = [
-    "open", "File", "Image", "INDEX_NAMES", "SAMPLED_INDICES", "ReadStats", "BACKENDS",
-    "Metadata", "Channel", "Quantity",
+    "open", "group_files", "FileGroup", "Grouping", "File", "Image", "INDEX_NAMES", "PLATE_INDICES", "SAMPLED_INDICES", "ReadStats",
+    "BACKENDS", "Metadata", "Channel", "Quantity", "Plate", "Well", "Field", "Acquisition",
     "decode_threads", "set_decode_threads", "memory_limit", "set_memory_limit",
     "cache_limit", "set_cache_limit", "cached_bytes",
     "MicroReaderError", "UnsupportedFormatError", "CorruptFileError", "MemoryLimitError", "DamagedFileWarning",
+    "MissingImagesWarning", "CompanionWarning", "CompositeWarning",
     "__version__",
 ]