From 4b0c1e8b70dc2551514a273a64057151029a1f6a Mon Sep 17 00:00:00 2001 From: Muhanad Zahra <86613209+muhanadz@users.noreply.github.com> Date: Thu, 7 Apr 2022 13:14:20 +0100 Subject: [PATCH 01/24] Updating README Updating README.rst to include the changes to default behaviour --- README.rst | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/README.rst b/README.rst index 1e568745..513df1fb 100644 --- a/README.rst +++ b/README.rst @@ -70,8 +70,12 @@ object IDs in the ``OMERO.table``. The ``CSV`` file must be provided as local file with ``--file path/to/file.csv``. -If you wish to ensure that ``number`` columns are created for numerical data, this will -allow you to make numerical queries on the table. + + +Automatic header +^^^^^^^^^ + +**The default behaviour of the script is to automatically detect the column types and specific object types from an input ``CSV`` using the list below.** Column Types are: - ``d``: ``DoubleColumn``, for floating point numbers @@ -80,8 +84,14 @@ Column Types are: - ``b``: ``BoolColumn``, for true/false - ``plate``, ``well``, ``image``, ``dataset``, ``roi`` to specify objects -These can be specified in the first row of a ``CSV`` with a ``# header`` tag (see examples below). -The ``# header`` row is optional. Default column type is ``String``. + + +Manual Header +^^^^^^^^^ + +However, it is possible to override the default behaviour, ignoring the automatic header detection, and manually assign the header to define the column type if a ``CSV`` with with a ``# header`` tag is passed (see examples below). + +Automatic header detection can also be ignored if using the ``--manual_headers`` flag. If the ``# header`` is not present and this flag is used, column types will default to ``String`` NB: Column names should not contain spaces if you want to be able to query by these columns. From 115dcbf77fca9a2c31da8286acadbd2fef05709a Mon Sep 17 00:00:00 2001 From: Muhanad Zahra <86613209+muhanadz@users.noreply.github.com> Date: Thu, 7 Apr 2022 13:16:08 +0100 Subject: [PATCH 02/24] Clearer titles --- README.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.rst b/README.rst index 513df1fb..c4347203 100644 --- a/README.rst +++ b/README.rst @@ -72,7 +72,7 @@ The ``CSV`` file must be provided as local file with ``--file path/to/file.csv`` -Automatic header +Automatic Column Types ^^^^^^^^^ **The default behaviour of the script is to automatically detect the column types and specific object types from an input ``CSV`` using the list below.** @@ -86,7 +86,7 @@ Column Types are: -Manual Header +Manual Column Types ^^^^^^^^^ However, it is possible to override the default behaviour, ignoring the automatic header detection, and manually assign the header to define the column type if a ``CSV`` with with a ``# header`` tag is passed (see examples below). From 0d291cc2263e0f5145c6a82c64b902b4bb13047e Mon Sep 17 00:00:00 2001 From: Muhanad Zahra <86613209+muhanadz@users.noreply.github.com> Date: Fri, 8 Apr 2022 11:04:31 +0100 Subject: [PATCH 03/24] Fixed grammer. Added more examples. Fixed grammer. Added more examples for automatic header detection. Added linkable titles to some headings --- README.rst | 64 +++++++++++++++++++++++++++++++++++++++--------------- 1 file changed, 46 insertions(+), 18 deletions(-) diff --git a/README.rst b/README.rst index c4347203..321747f6 100644 --- a/README.rst +++ b/README.rst @@ -71,10 +71,6 @@ object IDs in the ``OMERO.table``. The ``CSV`` file must be provided as local file with ``--file path/to/file.csv``. - -Automatic Column Types -^^^^^^^^^ - **The default behaviour of the script is to automatically detect the column types and specific object types from an input ``CSV`` using the list below.** Column Types are: @@ -85,25 +81,25 @@ Column Types are: - ``plate``, ``well``, ``image``, ``dataset``, ``roi`` to specify objects +However, it is possible to manually define the column types , ignoring the automatic header detection, if a ``CSV`` with a ``# header`` row is passed (see examples below). -Manual Column Types -^^^^^^^^^ - -However, it is possible to override the default behaviour, ignoring the automatic header detection, and manually assign the header to define the column type if a ``CSV`` with with a ``# header`` tag is passed (see examples below). - -Automatic header detection can also be ignored if using the ``--manual_headers`` flag. If the ``# header`` is not present and this flag is used, column types will default to ``String`` +Automatic header detection can also be ignored if using the ``--manual_headers`` flag. If the ``# header`` is not present and this flag is used, column types will default to ``String`` (unless the column names correspond to OMERO objects such as ``image`` or ``plate``). NB: Column names should not contain spaces if you want to be able to query by these columns. +Examples +^^^^^^^^^ + **Project / Dataset** +^^^^^^^^^ To add a table to a Project, the ``CSV`` file needs to specify ``Dataset Name`` and ``Image Name`` or ``Image ID``:: $ omero metadata populate Project:1 --file path/to/project.csv - -project.csv:: + +project.csv (manual column types definition):: # header s,s,d,l,s Image Name,Dataset Name,ROI_Area,Channel_Index,Channel_Name @@ -112,7 +108,15 @@ project.csv:: img-03.png,dataset01,0.093,3,TRITC img-04.png,dataset01,0.429,4,Cy5 -This will create an OMERO.table linked to the Project like this with +project.csv (automatic column types detection):: + + Image Name,Dataset Name,ROI_Area,Channel_Index,Channel_Name + img-01.png,dataset01,0.0469,1,DAPI + img-02.png,dataset01,0.142,2,GFP + img-03.png,dataset01,0.093,3,TRITC + img-04.png,dataset01,0.429,4,Cy5 + +Both manual definition or automatic detection of column types will create an OMERO.table linked to the Project as folows with a new ``Image`` column with IDs: ========== ============ ======== ============= ============ ===== @@ -128,11 +132,14 @@ If the target is a Dataset instead of a Project, the ``Dataset Name`` column is **Screen / Plate** +^^^^^^^^^ To add a table to a Screen, the ``CSV`` file needs to specify ``Plate`` name and ``Well``. -If a ``# header`` is specified, column types must be ``well`` and ``plate``. +If a ``# header`` is specified, column types must be ``well`` and ``plate``:: -screen.csv:: + $ omero metadata populate Screen:1 --file path/to/screen.csv + +screen.csv (manual column types definition):: # header well,plate,s,d,l,d Well,Plate,Drug,Concentration,Cell_Count,Percent_Mitotic @@ -141,7 +148,15 @@ screen.csv:: A3,plate01,DMSO,5.5,550,4 B1,plate01,DrugX,12.3,50,44.43 -This will create an OMERO.table linked to the Screen, with the +screen.csv (automatic column types detection):: + + Well,Plate,Drug,Concentration,Cell_Count,Percent_Mitotic + A1,plate01,DMSO,10.1,10,25.4 + A2,plate01,DMSO,0.1,1000,2.54 + A3,plate01,DMSO,5.5,550,4 + B1,plate01,DrugX,12.3,50,44.43 + +Similarly, this will create an OMERO.table linked to the Screen, with the ``Well Name`` and ``Plate Name`` columns added and the ``Well`` and ``Plate`` columns used for IDs: @@ -157,6 +172,7 @@ Well Plate Drug Concentration Cell_Count Percent_Mitotic Well Name Plat If the target is a Plate instead of a Screen, the ``Plate`` column is not needed. **ROIs** +^^^^^^^^^ If the target is an Image or a Dataset, a ``CSV`` with ROI-level or Shape-level data can be used to create an ``OMERO.table`` (bulk annotation) as a ``File Annotation`` linked to the target object. @@ -168,9 +184,11 @@ NB: Columns of type ``shape`` aren't yet supported on the OMERO.server. Alternatively, if the target is an Image, the ROI input column can be ``Roi Name`` (with type ``s``), and an ``roi`` type column will be appended containing ROI IDs. -In this case, it is required that ROIs on the Image in OMERO have the ``Name`` attribute set. +In this case, it is required that ROIs on the Image in OMERO have the ``Name`` attribute set:: -image.csv:: + $ omero metadata populate Image:1 --file path/to/image.csv + +image.csv (manual column types definition):: # header roi,l,l,d,l Roi,shape,object,probability,area @@ -179,6 +197,16 @@ image.csv:: 503,1068,3,0.2,25 503,1069,4,0.8,400 503,1070,5,0.5,200 + + +image.csv (automatic column types detection):: + + Roi,shape,object,probability,area + 501,1066,1,0.8,250 + 502,1067,2,0.9,500 + 503,1068,3,0.2,25 + 503,1069,4,0.8,400 + 503,1070,5,0.5,200 This will create an OMERO.table linked to the Image like this: From 494314a04b5b1f38eb3076b03edd740fd99a5423 Mon Sep 17 00:00:00 2001 From: Muhanad Zahra <86613209+muhanadz@users.noreply.github.com> Date: Fri, 8 Apr 2022 14:46:58 +0100 Subject: [PATCH 04/24] Improved clarify --- README.rst | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/README.rst b/README.rst index 321747f6..370597cf 100644 --- a/README.rst +++ b/README.rst @@ -70,19 +70,20 @@ object IDs in the ``OMERO.table``. The ``CSV`` file must be provided as local file with ``--file path/to/file.csv``. +OMERO.tables have defined column types to specify the data-type such as `double` or `long` and special object-types of each column for storing OMERO object IDs such as ``ImageColumn`` or ``WellColumn`` -**The default behaviour of the script is to automatically detect the column types and specific object types from an input ``CSV`` using the list below.** -Column Types are: +**The default behaviour of the script is to automatically detect these column types from an input ``CSV``**. This behaviour works as folows: +* Columns named with a supported object-type (e.g. 'image', 'plate'...) or with object_id (e.g. 'image_id', 'dataset_id' ) will generate the corresponding column type in the OMERO.table. e.g (ImageColumn, PlateColumn, DatasetColumn, etc) +* Other column types will be detected based on the column's data using the pandas library (e.g. column of data type double). + +However, it is possible to manually define the column types , ignoring the automatic header detection, if a ``CSV`` with a ``# header`` row is passed. The ``# header`` row should be the first row of the CSV and defines columns according to the following list (see examples below): - ``d``: ``DoubleColumn``, for floating point numbers - ``l``: ``LongColumn``, for integer numbers - ``s``: ``StringColumn``, for text - ``b``: ``BoolColumn``, for true/false - ``plate``, ``well``, ``image``, ``dataset``, ``roi`` to specify objects - -However, it is possible to manually define the column types , ignoring the automatic header detection, if a ``CSV`` with a ``# header`` row is passed (see examples below). - Automatic header detection can also be ignored if using the ``--manual_headers`` flag. If the ``# header`` is not present and this flag is used, column types will default to ``String`` (unless the column names correspond to OMERO objects such as ``image`` or ``plate``). NB: Column names should not contain spaces if you want to be able to query From 70a1c92a795759342cf4f98fe9d6c03ba85a0a19 Mon Sep 17 00:00:00 2001 From: Muhanad Zahra <86613209+muhanadz@users.noreply.github.com> Date: Fri, 8 Apr 2022 15:55:37 +0100 Subject: [PATCH 05/24] Fixed formatting --- README.rst | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/README.rst b/README.rst index 370597cf..02bb4455 100644 --- a/README.rst +++ b/README.rst @@ -73,8 +73,9 @@ The ``CSV`` file must be provided as local file with ``--file path/to/file.csv`` OMERO.tables have defined column types to specify the data-type such as `double` or `long` and special object-types of each column for storing OMERO object IDs such as ``ImageColumn`` or ``WellColumn`` **The default behaviour of the script is to automatically detect these column types from an input ``CSV``**. This behaviour works as folows: -* Columns named with a supported object-type (e.g. 'image', 'plate'...) or with object_id (e.g. 'image_id', 'dataset_id' ) will generate the corresponding column type in the OMERO.table. e.g (ImageColumn, PlateColumn, DatasetColumn, etc) -* Other column types will be detected based on the column's data using the pandas library (e.g. column of data type double). + +* Columns named with a supported object-type (e.g. 'image', 'plate'...) or with object_id (e.g. 'image_id', 'dataset_id' ) will generate the corresponding column type in the OMERO.table. e.g (ImageColumn, PlateColumn, DatasetColumn, etc) +* Other column types will be detected based on the column's data using the pandas library (e.g. column of data type double). However, it is possible to manually define the column types , ignoring the automatic header detection, if a ``CSV`` with a ``# header`` row is passed. The ``# header`` row should be the first row of the CSV and defines columns according to the following list (see examples below): From 2bc1a06aafd76f143d0c246e70ba940720e0df5e Mon Sep 17 00:00:00 2001 From: Muhanad Zahra <86613209+muhanadz@users.noreply.github.com> Date: Fri, 8 Apr 2022 15:57:41 +0100 Subject: [PATCH 06/24] Added full list for supported object-type --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 02bb4455..91830e7a 100644 --- a/README.rst +++ b/README.rst @@ -74,7 +74,7 @@ OMERO.tables have defined column types to specify the data-type such as `double` **The default behaviour of the script is to automatically detect these column types from an input ``CSV``**. This behaviour works as folows: -* Columns named with a supported object-type (e.g. 'image', 'plate'...) or with object_id (e.g. 'image_id', 'dataset_id' ) will generate the corresponding column type in the OMERO.table. e.g (ImageColumn, PlateColumn, DatasetColumn, etc) +* Columns named with a supported object-type ('plate', 'well', 'image', 'dataset', or 'roi') or with object_id (e.g. 'image_id', 'dataset_id') will generate the corresponding column type in the OMERO.table. e.g (ImageColumn, PlateColumn, DatasetColumn, etc) * Other column types will be detected based on the column's data using the pandas library (e.g. column of data type double). From f6610a20bbb6914c5843474f2e80d46b9bf8c92d Mon Sep 17 00:00:00 2001 From: Muhanad Zahra <86613209+muhanadz@users.noreply.github.com> Date: Fri, 15 Apr 2022 14:21:03 +0100 Subject: [PATCH 07/24] Updating linting --- README.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/README.rst b/README.rst index 91830e7a..d8f33849 100644 --- a/README.rst +++ b/README.rst @@ -79,6 +79,7 @@ OMERO.tables have defined column types to specify the data-type such as `double` However, it is possible to manually define the column types , ignoring the automatic header detection, if a ``CSV`` with a ``# header`` row is passed. The ``# header`` row should be the first row of the CSV and defines columns according to the following list (see examples below): + - ``d``: ``DoubleColumn``, for floating point numbers - ``l``: ``LongColumn``, for integer numbers - ``s``: ``StringColumn``, for text From 0cc977f9c4d2309b8712f2ef20ad93cba68295f2 Mon Sep 17 00:00:00 2001 From: Muhanad Zahra <86613209+muhanadz@users.noreply.github.com> Date: Fri, 15 Apr 2022 16:00:17 +0100 Subject: [PATCH 08/24] Fixed Title underline too short --- README.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.rst b/README.rst index d8f33849..9f4aa6a8 100644 --- a/README.rst +++ b/README.rst @@ -95,7 +95,7 @@ Examples ^^^^^^^^^ **Project / Dataset** -^^^^^^^^^ +^^^^^^^^^^^^^^^^^^^^^^ To add a table to a Project, the ``CSV`` file needs to specify ``Dataset Name`` and ``Image Name`` or ``Image ID``:: @@ -135,7 +135,7 @@ If the target is a Dataset instead of a Project, the ``Dataset Name`` column is **Screen / Plate** -^^^^^^^^^ +^^^^^^^^^^^^^^^^^^^ To add a table to a Screen, the ``CSV`` file needs to specify ``Plate`` name and ``Well``. If a ``# header`` is specified, column types must be ``well`` and ``plate``:: From b3610bcad0ea9cf58543eec14be9b9fe0f2d5b89 Mon Sep 17 00:00:00 2001 From: Muhanad Zahra <86613209+muhanadz@users.noreply.github.com> Date: Mon, 18 Apr 2022 16:05:05 +0100 Subject: [PATCH 09/24] removed double star Co-authored-by: pwalczysko --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 9f4aa6a8..c154563d 100644 --- a/README.rst +++ b/README.rst @@ -72,7 +72,7 @@ The ``CSV`` file must be provided as local file with ``--file path/to/file.csv`` OMERO.tables have defined column types to specify the data-type such as `double` or `long` and special object-types of each column for storing OMERO object IDs such as ``ImageColumn`` or ``WellColumn`` -**The default behaviour of the script is to automatically detect these column types from an input ``CSV``**. This behaviour works as folows: +The default behaviour of the script is to ``automatically detect these column types`` from an input ``CSV``. This behaviour works as folows: * Columns named with a supported object-type ('plate', 'well', 'image', 'dataset', or 'roi') or with object_id (e.g. 'image_id', 'dataset_id') will generate the corresponding column type in the OMERO.table. e.g (ImageColumn, PlateColumn, DatasetColumn, etc) * Other column types will be detected based on the column's data using the pandas library (e.g. column of data type double). From bf24a6b7c1ffabe231e9da83c0e3e0f5b30f35eb Mon Sep 17 00:00:00 2001 From: Muhanad Zahra <86613209+muhanadz@users.noreply.github.com> Date: Mon, 18 Apr 2022 16:14:12 +0100 Subject: [PATCH 10/24] Removed extra backticks --- README.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.rst b/README.rst index c154563d..bfac6f80 100644 --- a/README.rst +++ b/README.rst @@ -70,9 +70,9 @@ object IDs in the ``OMERO.table``. The ``CSV`` file must be provided as local file with ``--file path/to/file.csv``. -OMERO.tables have defined column types to specify the data-type such as `double` or `long` and special object-types of each column for storing OMERO object IDs such as ``ImageColumn`` or ``WellColumn`` +OMERO.tables have defined column types to specify the data-type such as ``double`` or ``long`` and special object-types of each column for storing OMERO object IDs such as ``ImageColumn`` or ``WellColumn`` -The default behaviour of the script is to ``automatically detect these column types`` from an input ``CSV``. This behaviour works as folows: +The default behaviour of the script is to automatically detect the column types from an input ``CSV``. This behaviour works as folows: * Columns named with a supported object-type ('plate', 'well', 'image', 'dataset', or 'roi') or with object_id (e.g. 'image_id', 'dataset_id') will generate the corresponding column type in the OMERO.table. e.g (ImageColumn, PlateColumn, DatasetColumn, etc) * Other column types will be detected based on the column's data using the pandas library (e.g. column of data type double). From fcbc1c8a63fad20aec91560bbc93bc948b87816e Mon Sep 17 00:00:00 2001 From: Muhanad Zahra <86613209+muhanadz@users.noreply.github.com> Date: Thu, 12 May 2022 11:12:27 +0100 Subject: [PATCH 11/24] Added dataset id example --- README.rst | 34 ++++++++++++++++++++++++++++++++-- 1 file changed, 32 insertions(+), 2 deletions(-) diff --git a/README.rst b/README.rst index bfac6f80..20fd176a 100644 --- a/README.rst +++ b/README.rst @@ -97,7 +97,7 @@ Examples **Project / Dataset** ^^^^^^^^^^^^^^^^^^^^^^ -To add a table to a Project, the ``CSV`` file needs to specify ``Dataset Name`` +To add a table to a Project, the ``CSV`` file needs to specify ``Dataset Name`` or ``Dataset ID`` and ``Image Name`` or ``Image ID``:: $ omero metadata populate Project:1 --file path/to/project.csv @@ -131,8 +131,38 @@ img-03.png dataset01 0.093 3 TRITC 36640 img-04.png dataset01 0.429 4 Cy5 36641 ========== ============ ======== ============= ============ ===== -If the target is a Dataset instead of a Project, the ``Dataset Name`` column is not needed. +Example using ``Image ID`` and ``Dataset ID``. + +project.csv (manual column types definition):: + + # header image,dataset,d,l,s + image id,Dataset ID,ROI_Area,Channel_Index,Channel_Name + 36638,101,0.0469,1,DAPI + 36639,101,0.142,2,GFP + 36640,101,0.093,3,TRITC + 36641,101,0.429,4,Cy5 + +project.csv (automatic column types detection):: + image id,Dataset ID,ROI_Area,Channel_Index,Channel_Name + 36638,101,0.0469,1,DAPI + 36639,101,0.142,2,GFP + 36640,101,0.093,3,TRITC + 36641,101,0.429,4,Cy5 + +Both manual definition or automatic detection of column types will create an OMERO.table linked to the Project as folows with +a new ``Image`` column with Names: + +===== ======= ======== ============= ============ ========== +Image Dataset ROI_Area Channel_Index Channel_Name Image Name +===== ======= ======== ============= ============ ========== +36638 101 0.0469 1 DAPI img-01.png +36639 101 0.142 2 GFP img-02.png +36640 101 0.093 3 TRITC img-03.png +36641 101 0.429 4 Cy5 img-04.png +===== ======= ======== ============= ============ ========== + +If the target is a Dataset instead of a Project, the ``Dataset Name`` column is not needed. **Screen / Plate** ^^^^^^^^^^^^^^^^^^^ From 6c5500b60b648e3f3f7de86e01af53d18df22bb5 Mon Sep 17 00:00:00 2001 From: Muhanad Zahra <86613209+muhanadz@users.noreply.github.com> Date: Thu, 12 May 2022 11:38:28 +0100 Subject: [PATCH 12/24] fixing language --- README.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.rst b/README.rst index 20fd176a..c157d3b5 100644 --- a/README.rst +++ b/README.rst @@ -74,8 +74,8 @@ OMERO.tables have defined column types to specify the data-type such as ``double The default behaviour of the script is to automatically detect the column types from an input ``CSV``. This behaviour works as folows: -* Columns named with a supported object-type ('plate', 'well', 'image', 'dataset', or 'roi') or with object_id (e.g. 'image_id', 'dataset_id') will generate the corresponding column type in the OMERO.table. e.g (ImageColumn, PlateColumn, DatasetColumn, etc) -* Other column types will be detected based on the column's data using the pandas library (e.g. column of data type double). +* Columns named with a supported object-type (e.g. 'plate', 'well', 'image', 'dataset', or 'roi'), with _id (e.g. 'image_id', 'dataset_id') or with _name (e.g. 'plate_name', 'dataset_name') will generate the corresponding column type in the OMERO.table (e.g. ImageColumn, PlateColumn, DatasetColumn, etc). +* All other column types will be detected based on the column's data using the pandas library (e.g. columns of data type double will be detected as ``DoubleColumn``). However, it is possible to manually define the column types , ignoring the automatic header detection, if a ``CSV`` with a ``# header`` row is passed. The ``# header`` row should be the first row of the CSV and defines columns according to the following list (see examples below): @@ -150,7 +150,7 @@ project.csv (automatic column types detection):: 36640,101,0.093,3,TRITC 36641,101,0.429,4,Cy5 -Both manual definition or automatic detection of column types will create an OMERO.table linked to the Project as folows with +The previous example will create an OMERO.table linked to the Project as folows with a new ``Image`` column with Names: ===== ======= ======== ============= ============ ========== @@ -189,7 +189,7 @@ screen.csv (automatic column types detection):: A3,plate01,DMSO,5.5,550,4 B1,plate01,DrugX,12.3,50,44.43 -Similarly, this will create an OMERO.table linked to the Screen, with the +This will create an OMERO.table linked to the Screen, with the ``Well Name`` and ``Plate Name`` columns added and the ``Well`` and ``Plate`` columns used for IDs: From 30c22fe4afaddca7ab82162793a8d661b7bf57fb Mon Sep 17 00:00:00 2001 From: Muhanad Zahra <86613209+muhanadz@users.noreply.github.com> Date: Tue, 17 May 2022 14:48:14 +0100 Subject: [PATCH 13/24] Updated workding. Added documented table. Removed some of the complex wording and replaced it with a table in a form of documentation. --- README.rst | 88 +++++++++++++++++++++++++++++------------------------- 1 file changed, 47 insertions(+), 41 deletions(-) diff --git a/README.rst b/README.rst index c157d3b5..945c9993 100644 --- a/README.rst +++ b/README.rst @@ -64,7 +64,7 @@ populate -------- This command creates an ``OMERO.table`` (bulk annotation) from a ``CSV`` file and links -the table as a ``File Annotation`` to a parent container such as Screen, Plate, Project +the table as a ``File Annotation`` to a parent container such as Screen, Plate, Project, Dataset or Image. It also attempts to convert Image, Well or ROI names from the ``CSV`` into object IDs in the ``OMERO.table``. @@ -72,13 +72,45 @@ The ``CSV`` file must be provided as local file with ``--file path/to/file.csv`` OMERO.tables have defined column types to specify the data-type such as ``double`` or ``long`` and special object-types of each column for storing OMERO object IDs such as ``ImageColumn`` or ``WellColumn`` -The default behaviour of the script is to automatically detect the column types from an input ``CSV``. This behaviour works as folows: - -* Columns named with a supported object-type (e.g. 'plate', 'well', 'image', 'dataset', or 'roi'), with _id (e.g. 'image_id', 'dataset_id') or with _name (e.g. 'plate_name', 'dataset_name') will generate the corresponding column type in the OMERO.table (e.g. ImageColumn, PlateColumn, DatasetColumn, etc). -* All other column types will be detected based on the column's data using the pandas library (e.g. columns of data type double will be detected as ``DoubleColumn``). - - -However, it is possible to manually define the column types , ignoring the automatic header detection, if a ``CSV`` with a ``# header`` row is passed. The ``# header`` row should be the first row of the CSV and defines columns according to the following list (see examples below): +The default behaviour of the script is to automatically detect the column types from an input ``CSV``. This behaviour works as follows: + +* Columns named with a supported object-type (e.g. ``plate``, ``well``, ``image``, ``dataset``, or ``roi``), with ``_id`` or ``_name`` will generate the corresponding column type in the OMERO.table. See table below for full list of supported column names. + +============ ================= ==================== ================================== +Column Name Column type Detected Header Type Notes +============ ================= ==================== ================================== +Image ``ImageColumn`` ``image`` Appends 'Image Name' column +Image Name ``StringColumn`` ``s`` Appends 'Image' column +Image ID ``ImageColumn`` ``image`` Appends 'Image Name' column +Dataset ``DatasetColumn`` ``dataset`` \- +Dataset Name ``StringColumn`` ``s`` \- +Dataset ID ``DatasetColumn`` ``dataset`` \- +Plate ``PlateColumn`` ``plate`` Adds 'Plate' column +Plate Name ``PlateColumn`` ``plate`` Adds 'Plate' column +Plate ID ``LongColumn`` ``l`` \- +Well ``WellColumn`` ``well`` Adds 'Well' column +Well Name ``WellColumn`` ``well`` Adds 'Well' column +Well ID ``LongColumn`` ``l`` \- +ROI ``RoiColumn`` ``roi`` Appends 'ROI Name' column +ROI Name ``StringColumn`` ``s`` \- +ROI ID ``RoiColumn`` ``roi`` Appends 'ROI Name' column +============ ================= ==================== ================================== + +Note: Column names are case insensitive. Space, nospace, and underscore are all accepted as seperaters for column names (i.e. `` name``/`` id```, ``name``/``id``, ``_name``/``_id`` are all accepted) + +* All other column types will be detected based on the column's data using the pandas library. See table below. + +=============== ================= ==================== +Column Name Column type Detected Header Type +=============== ================= ==================== +Example String ``StringColumn`` ``s`` +Example Long ``LongColumn`` ``l`` +Example Float ``DoubleColumn`` ``d`` +Example boolean ``BoolColumn`` ``b`` +=============== ================= ==================== + + +However, it is possible to manually define the header types, ignoring the automatic header detection, if a ``CSV`` with a ``# header`` row is passed. The ``# header`` row should be the first row of the CSV and defines columns according to the following list (see examples below): - ``d``: ``DoubleColumn``, for floating point numbers - ``l``: ``LongColumn``, for integer numbers @@ -110,16 +142,10 @@ project.csv (manual column types definition):: img-02.png,dataset01,0.142,2,GFP img-03.png,dataset01,0.093,3,TRITC img-04.png,dataset01,0.429,4,Cy5 + +Note: Remove ``# header`` row for automatic column types detection. -project.csv (automatic column types detection):: - - Image Name,Dataset Name,ROI_Area,Channel_Index,Channel_Name - img-01.png,dataset01,0.0469,1,DAPI - img-02.png,dataset01,0.142,2,GFP - img-03.png,dataset01,0.093,3,TRITC - img-04.png,dataset01,0.429,4,Cy5 - -Both manual definition or automatic detection of column types will create an OMERO.table linked to the Project as folows with +Both manual definition or automatic detection of column types will create an OMERO.table linked to the Project as follows with a new ``Image`` column with IDs: ========== ============ ======== ============= ============ ===== @@ -141,16 +167,10 @@ project.csv (manual column types definition):: 36639,101,0.142,2,GFP 36640,101,0.093,3,TRITC 36641,101,0.429,4,Cy5 - -project.csv (automatic column types detection):: - image id,Dataset ID,ROI_Area,Channel_Index,Channel_Name - 36638,101,0.0469,1,DAPI - 36639,101,0.142,2,GFP - 36640,101,0.093,3,TRITC - 36641,101,0.429,4,Cy5 +Note: Remove ``# header`` row for automatic column types detection. -The previous example will create an OMERO.table linked to the Project as folows with +The previous example will create an OMERO.table linked to the Project as follows with a new ``Image`` column with Names: ===== ======= ======== ============= ============ ========== @@ -181,13 +201,7 @@ screen.csv (manual column types definition):: A3,plate01,DMSO,5.5,550,4 B1,plate01,DrugX,12.3,50,44.43 -screen.csv (automatic column types detection):: - - Well,Plate,Drug,Concentration,Cell_Count,Percent_Mitotic - A1,plate01,DMSO,10.1,10,25.4 - A2,plate01,DMSO,0.1,1000,2.54 - A3,plate01,DMSO,5.5,550,4 - B1,plate01,DrugX,12.3,50,44.43 +Note: Remove ``# header`` row for automatic column types detection. This will create an OMERO.table linked to the Screen, with the ``Well Name`` and ``Plate Name`` columns added and the ``Well`` and @@ -231,15 +245,7 @@ image.csv (manual column types definition):: 503,1069,4,0.8,400 503,1070,5,0.5,200 - -image.csv (automatic column types detection):: - - Roi,shape,object,probability,area - 501,1066,1,0.8,250 - 502,1067,2,0.9,500 - 503,1068,3,0.2,25 - 503,1069,4,0.8,400 - 503,1070,5,0.5,200 +Note: Remove ``# header`` row for automatic column types detection. This will create an OMERO.table linked to the Image like this: From 9db1280527b460a30da26f6cca345a3d4cdd7677 Mon Sep 17 00:00:00 2001 From: Muhanad Zahra <86613209+muhanadz@users.noreply.github.com> Date: Wed, 25 May 2022 16:28:52 +0100 Subject: [PATCH 14/24] Fixed formatting and concise wording --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 945c9993..bd1816d8 100644 --- a/README.rst +++ b/README.rst @@ -36,7 +36,7 @@ conflicts when importing the Python module. Usage ===== -The plugin is called from the command-line using the `omero` command:: +The plugin is called from the command-line using the ``omero metadata`` command:: $ omero metadata From 2e6e7cf76f9223ba9d9eb1b935df92c277010c32 Mon Sep 17 00:00:00 2001 From: Muhanad Zahra <86613209+muhanadz@users.noreply.github.com> Date: Wed, 25 May 2022 16:30:33 +0100 Subject: [PATCH 15/24] Consistent wording --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index bd1816d8..4c1842f0 100644 --- a/README.rst +++ b/README.rst @@ -74,7 +74,7 @@ OMERO.tables have defined column types to specify the data-type such as ``double The default behaviour of the script is to automatically detect the column types from an input ``CSV``. This behaviour works as follows: -* Columns named with a supported object-type (e.g. ``plate``, ``well``, ``image``, ``dataset``, or ``roi``), with ``_id`` or ``_name`` will generate the corresponding column type in the OMERO.table. See table below for full list of supported column names. +* Columns named with a supported object-type (e.g. ``plate``, ``well``, ``image``, ``dataset``, or ``roi``), with `` id`` or `` name`` will generate the corresponding column type in the OMERO.table. See table below for full list of supported column names. ============ ================= ==================== ================================== Column Name Column type Detected Header Type Notes From 42ca428587413aa137fab3f2afe5252f675f6658 Mon Sep 17 00:00:00 2001 From: Muhanad Zahra <86613209+muhanadz@users.noreply.github.com> Date: Wed, 25 May 2022 17:11:56 +0100 Subject: [PATCH 16/24] Reverted the paradigm the examples now show the default behavior instead of the manual selection. --- README.rst | 35 ++++++++++++++++++++--------------- 1 file changed, 20 insertions(+), 15 deletions(-) diff --git a/README.rst b/README.rst index 4c1842f0..4504bb6b 100644 --- a/README.rst +++ b/README.rst @@ -123,9 +123,12 @@ Automatic header detection can also be ignored if using the ``--manual_headers`` NB: Column names should not contain spaces if you want to be able to query by these columns. + Examples ^^^^^^^^^ +The examples below will use the default automatic column types detection behaviour. It is possible to achieve the same results (or a different desired result) by manually adding a custom ``# header`` row at the top of the CSV. + **Project / Dataset** ^^^^^^^^^^^^^^^^^^^^^^ @@ -134,18 +137,18 @@ and ``Image Name`` or ``Image ID``:: $ omero metadata populate Project:1 --file path/to/project.csv -project.csv (manual column types definition):: +Using ``Image Name`` and ``Dataset Name``: + +project.csv:: - # header s,s,d,l,s Image Name,Dataset Name,ROI_Area,Channel_Index,Channel_Name img-01.png,dataset01,0.0469,1,DAPI img-02.png,dataset01,0.142,2,GFP img-03.png,dataset01,0.093,3,TRITC img-04.png,dataset01,0.429,4,Cy5 -Note: Remove ``# header`` row for automatic column types detection. -Both manual definition or automatic detection of column types will create an OMERO.table linked to the Project as follows with +The previous example will create an OMERO.table linked to the Project as follows with a new ``Image`` column with IDs: ========== ============ ======== ============= ============ ===== @@ -157,19 +160,19 @@ img-03.png dataset01 0.093 3 TRITC 36640 img-04.png dataset01 0.429 4 Cy5 36641 ========== ============ ======== ============= ============ ===== -Example using ``Image ID`` and ``Dataset ID``. +Note: equivalent to adding ``# header s,s,d,l,s`` row to the top of the ``project.csv`` for manual definition. + +Using ``Image ID`` and ``Dataset ID``: -project.csv (manual column types definition):: +project.csv:: - # header image,dataset,d,l,s image id,Dataset ID,ROI_Area,Channel_Index,Channel_Name 36638,101,0.0469,1,DAPI 36639,101,0.142,2,GFP 36640,101,0.093,3,TRITC 36641,101,0.429,4,Cy5 -Note: Remove ``# header`` row for automatic column types detection. - + The previous example will create an OMERO.table linked to the Project as follows with a new ``Image`` column with Names: @@ -184,6 +187,8 @@ Image Dataset ROI_Area Channel_Index Channel_Name Image Name If the target is a Dataset instead of a Project, the ``Dataset Name`` column is not needed. +Note: equivalent to adding ``# header image,dataset,d,l,s`` row to the top of the ``project.csv`` for manual definition. + **Screen / Plate** ^^^^^^^^^^^^^^^^^^^ @@ -192,16 +197,14 @@ If a ``# header`` is specified, column types must be ``well`` and ``plate``:: $ omero metadata populate Screen:1 --file path/to/screen.csv -screen.csv (manual column types definition):: +screen.csv:: - # header well,plate,s,d,l,d Well,Plate,Drug,Concentration,Cell_Count,Percent_Mitotic A1,plate01,DMSO,10.1,10,25.4 A2,plate01,DMSO,0.1,1000,2.54 A3,plate01,DMSO,5.5,550,4 B1,plate01,DrugX,12.3,50,44.43 -Note: Remove ``# header`` row for automatic column types detection. This will create an OMERO.table linked to the Screen, with the ``Well Name`` and ``Plate Name`` columns added and the ``Well`` and @@ -218,6 +221,8 @@ Well Plate Drug Concentration Cell_Count Percent_Mitotic Well Name Plat If the target is a Plate instead of a Screen, the ``Plate`` column is not needed. +Note: equivalent to adding ``# header well,plate,s,d,l,d`` row to the top of the ``screen.csv`` for manual definition. + **ROIs** ^^^^^^^^^ @@ -235,9 +240,8 @@ In this case, it is required that ROIs on the Image in OMERO have the ``Name`` a $ omero metadata populate Image:1 --file path/to/image.csv -image.csv (manual column types definition):: +image.csv:: - # header roi,l,l,d,l Roi,shape,object,probability,area 501,1066,1,0.8,250 502,1067,2,0.9,500 @@ -245,7 +249,6 @@ image.csv (manual column types definition):: 503,1069,4,0.8,400 503,1070,5,0.5,200 -Note: Remove ``# header`` row for automatic column types detection. This will create an OMERO.table linked to the Image like this: @@ -259,6 +262,8 @@ Roi shape object probability area Roi Name 503 1070 5 0.5 200 Sample3 === ===== ====== =========== ==== ======== +Note: equivalent to adding ``# header roi,l,l,d,l`` row to the top of the ``image.csv`` for manual definition. + Note that the ROI-level data from an ``OMERO.table`` is not visible in the OMERO.web UI right-hand panel under the ``Tables`` tab, but the table can be visualized by clicking the "eye" on the bulk annotation attachment on the Image. From b36691eacad2463b813b017d551259cc99392458 Mon Sep 17 00:00:00 2001 From: Muhanad Zahra <86613209+muhanadz@users.noreply.github.com> Date: Wed, 1 Jun 2022 23:12:51 +0100 Subject: [PATCH 17/24] Moved column name space warning earlier --- README.rst | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/README.rst b/README.rst index 4504bb6b..96fe7c0b 100644 --- a/README.rst +++ b/README.rst @@ -98,6 +98,8 @@ ROI ID ``RoiColumn`` ``roi`` Appends 'ROI Name' column Note: Column names are case insensitive. Space, nospace, and underscore are all accepted as seperaters for column names (i.e. `` name``/`` id```, ``name``/``id``, ``_name``/``_id`` are all accepted) +NB: Column names should not contain spaces if you want to be able to query by these columns. + * All other column types will be detected based on the column's data using the pandas library. See table below. =============== ================= ==================== @@ -120,9 +122,6 @@ However, it is possible to manually define the header types, ignoring the automa Automatic header detection can also be ignored if using the ``--manual_headers`` flag. If the ``# header`` is not present and this flag is used, column types will default to ``String`` (unless the column names correspond to OMERO objects such as ``image`` or ``plate``). -NB: Column names should not contain spaces if you want to be able to query -by these columns. - Examples ^^^^^^^^^ From 29a81030ddabbf628c9e2bcdefb4b5d80d47ea46 Mon Sep 17 00:00:00 2001 From: Muhanad Zahra <86613209+muhanadz@users.noreply.github.com> Date: Wed, 1 Jun 2022 23:20:48 +0100 Subject: [PATCH 18/24] Moved paragraph to avoid confusion --- README.rst | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/README.rst b/README.rst index 96fe7c0b..b3acdb38 100644 --- a/README.rst +++ b/README.rst @@ -231,11 +231,7 @@ If there is an ``roi`` column (header type ``roi``) containing ROI IDs, an ``Roi column will be appended automatically (see example below). If a column of Shape IDs named ``shape`` of type ``l`` is included, the Shape IDs will be validated (and set to -1 if invalid). Also if an ``image`` column of Image IDs is included, an ``Image Name`` column will be added. -NB: Columns of type ``shape`` aren't yet supported on the OMERO.server. - -Alternatively, if the target is an Image, the ROI input column can be -``Roi Name`` (with type ``s``), and an ``roi`` type column will be appended containing ROI IDs. -In this case, it is required that ROIs on the Image in OMERO have the ``Name`` attribute set:: +NB: Columns of type ``shape`` aren't yet supported on the OMERO.server:: $ omero metadata populate Image:1 --file path/to/image.csv @@ -263,6 +259,10 @@ Roi shape object probability area Roi Name Note: equivalent to adding ``# header roi,l,l,d,l`` row to the top of the ``image.csv`` for manual definition. +Alternatively, if the target is an Image, the ROI input column can be +``Roi Name`` (with type ``s``), and an ``roi`` type column will be appended containing ROI IDs. +In this case, it is required that ROIs on the Image in OMERO have the ``Name`` attribute set. + Note that the ROI-level data from an ``OMERO.table`` is not visible in the OMERO.web UI right-hand panel under the ``Tables`` tab, but the table can be visualized by clicking the "eye" on the bulk annotation attachment on the Image. From 08bd5d842cb5c027aa821f88cd306e9ee54b878c Mon Sep 17 00:00:00 2001 From: Muhanad Zahra <86613209+muhanadz@users.noreply.github.com> Date: Wed, 1 Jun 2022 23:44:11 +0100 Subject: [PATCH 19/24] Updated README --- README.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.rst b/README.rst index b3acdb38..469324b1 100644 --- a/README.rst +++ b/README.rst @@ -173,7 +173,7 @@ project.csv:: The previous example will create an OMERO.table linked to the Project as follows with -a new ``Image`` column with Names: +a new ``Image Name`` column with Names: ===== ======= ======== ============= ============ ========== Image Dataset ROI_Area Channel_Index Channel_Name Image Name @@ -285,4 +285,4 @@ licensed under the terms of the GNU General Public License (GPL) v2 or later. Copyright --------- -2018-2021, The Open Microscopy Environment +2018-2022, The Open Microscopy Environment and Glencoe Software, Inc From f8bcffdb02e62f1a127193824f95b866a9178d99 Mon Sep 17 00:00:00 2001 From: Muhanad Zahra <86613209+muhanadz@users.noreply.github.com> Date: Wed, 1 Jun 2022 23:48:34 +0100 Subject: [PATCH 20/24] Updated supported object-type table --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 469324b1..a9415b00 100644 --- a/README.rst +++ b/README.rst @@ -92,7 +92,7 @@ Well ``WellColumn`` ``well`` Adds 'Well' column Well Name ``WellColumn`` ``well`` Adds 'Well' column Well ID ``LongColumn`` ``l`` \- ROI ``RoiColumn`` ``roi`` Appends 'ROI Name' column -ROI Name ``StringColumn`` ``s`` \- +ROI Name ``StringColumn`` ``s`` Appends 'ROI' column ROI ID ``RoiColumn`` ``roi`` Appends 'ROI Name' column ============ ================= ==================== ================================== From 9c346f5924e9a04effcf5a6b732cfb2bd52f5377 Mon Sep 17 00:00:00 2001 From: Muhanad Zahra <86613209+muhanadz@users.noreply.github.com> Date: Wed, 1 Jun 2022 23:51:23 +0100 Subject: [PATCH 21/24] Fixed spelling Co-authored-by: pwalczysko --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index a9415b00..b6a8be62 100644 --- a/README.rst +++ b/README.rst @@ -96,7 +96,7 @@ ROI Name ``StringColumn`` ``s`` Appends 'ROI' column ROI ID ``RoiColumn`` ``roi`` Appends 'ROI Name' column ============ ================= ==================== ================================== -Note: Column names are case insensitive. Space, nospace, and underscore are all accepted as seperaters for column names (i.e. `` name``/`` id```, ``name``/``id``, ``_name``/``_id`` are all accepted) +Note: Column names are case insensitive. Space, no space, and underscore are all accepted as separators for column names (i.e. `` name``/`` id```, ``name``/``id``, ``_name``/``_id`` are all accepted) NB: Column names should not contain spaces if you want to be able to query by these columns. From 12cac5b5f3b560443099d2b9a94dc8e5cffdf323 Mon Sep 17 00:00:00 2001 From: Muhanad Zahra <86613209+muhanadz@users.noreply.github.com> Date: Thu, 2 Jun 2022 00:00:40 +0100 Subject: [PATCH 22/24] Updated alternative target object explanation --- README.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.rst b/README.rst index b6a8be62..bda9d143 100644 --- a/README.rst +++ b/README.rst @@ -184,10 +184,10 @@ Image Dataset ROI_Area Channel_Index Channel_Name Image Name 36641 101 0.429 4 Cy5 img-04.png ===== ======= ======== ============= ============ ========== -If the target is a Dataset instead of a Project, the ``Dataset Name`` column is not needed. - Note: equivalent to adding ``# header image,dataset,d,l,s`` row to the top of the ``project.csv`` for manual definition. +For both examples above, alternatively, if the target is a Dataset instead of a Project, the ``Dataset`` or ``Dataset Name`` column is not needed. + **Screen / Plate** ^^^^^^^^^^^^^^^^^^^ From 04eda4ef665681a3ee54b03bceed65d3291505af Mon Sep 17 00:00:00 2001 From: Muhanad Zahra <86613209+muhanadz@users.noreply.github.com> Date: Thu, 2 Jun 2022 00:29:28 +0100 Subject: [PATCH 23/24] Added more info to object-types table --- README.rst | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/README.rst b/README.rst index bda9d143..ad15a5df 100644 --- a/README.rst +++ b/README.rst @@ -76,25 +76,25 @@ The default behaviour of the script is to automatically detect the column types * Columns named with a supported object-type (e.g. ``plate``, ``well``, ``image``, ``dataset``, or ``roi``), with `` id`` or `` name`` will generate the corresponding column type in the OMERO.table. See table below for full list of supported column names. -============ ================= ==================== ================================== +============ ================= ==================== ==================================================================== Column Name Column type Detected Header Type Notes -============ ================= ==================== ================================== -Image ``ImageColumn`` ``image`` Appends 'Image Name' column -Image Name ``StringColumn`` ``s`` Appends 'Image' column -Image ID ``ImageColumn`` ``image`` Appends 'Image Name' column -Dataset ``DatasetColumn`` ``dataset`` \- -Dataset Name ``StringColumn`` ``s`` \- -Dataset ID ``DatasetColumn`` ``dataset`` \- -Plate ``PlateColumn`` ``plate`` Adds 'Plate' column -Plate Name ``PlateColumn`` ``plate`` Adds 'Plate' column -Plate ID ``LongColumn`` ``l`` \- -Well ``WellColumn`` ``well`` Adds 'Well' column -Well Name ``WellColumn`` ``well`` Adds 'Well' column -Well ID ``LongColumn`` ``l`` \- -ROI ``RoiColumn`` ``roi`` Appends 'ROI Name' column -ROI Name ``StringColumn`` ``s`` Appends 'ROI' column -ROI ID ``RoiColumn`` ``roi`` Appends 'ROI Name' column -============ ================= ==================== ================================== +============ ================= ==================== ==================================================================== +Image ``ImageColumn`` ``image`` Accepts image IDs. Appends new 'Image Name' column with image names. +Image Name ``StringColumn`` ``s`` Accepts image names. Appends new 'Image' column with image IDs. +Image ID ``ImageColumn`` ``image`` Accepts image IDs. Appends new 'Image Name' column with image names. +Dataset ``DatasetColumn`` ``dataset`` Accepts dataset IDs. +Dataset Name ``StringColumn`` ``s`` Accepts dataset names. +Dataset ID ``DatasetColumn`` ``dataset`` Accepts dataset IDs. +Plate ``PlateColumn`` ``plate`` Accepts plate names. Adds new 'Plate' column with plate IDs. +Plate Name ``PlateColumn`` ``plate`` Accepts plate names. Adds new 'Plate' column with plate IDs. +Plate ID ``LongColumn`` ``l`` Accepts plate IDs. +Well ``WellColumn`` ``well`` Accepts well names. Adds new 'Well' column with well IDs. +Well Name ``WellColumn`` ``well`` Accepts well names. Adds new 'Well' column with well IDs. +Well ID ``LongColumn`` ``l`` Accepts well IDs. +ROI ``RoiColumn`` ``roi`` Accepts ROI IDs. Appends new 'ROI Name' column with ROI names. +ROI Name ``StringColumn`` ``s`` Accepts ROI names. Appends new 'ROI' column with ROI IDs. +ROI ID ``RoiColumn`` ``roi`` Accepts ROI IDs. Appends new 'ROI Name' column with ROI names. +============ ================= ==================== ==================================================================== Note: Column names are case insensitive. Space, no space, and underscore are all accepted as separators for column names (i.e. `` name``/`` id```, ``name``/``id``, ``_name``/``_id`` are all accepted) From c6573afb734c13cc98d491c33156e1e7e6095348 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Besson?= Date: Tue, 21 Jun 2022 12:02:20 +0100 Subject: [PATCH 24/24] Update README.rst Co-authored-by: pwalczysko --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index ad15a5df..a4bd3241 100644 --- a/README.rst +++ b/README.rst @@ -70,7 +70,7 @@ object IDs in the ``OMERO.table``. The ``CSV`` file must be provided as local file with ``--file path/to/file.csv``. -OMERO.tables have defined column types to specify the data-type such as ``double`` or ``long`` and special object-types of each column for storing OMERO object IDs such as ``ImageColumn`` or ``WellColumn`` +OMERO.tables have defined column types to specify the data-type such as ``double`` or ``long`` and special object-types of each column for storing OMERO object IDs such as ``ImageColumn`` or ``WellColumn``. The default behaviour of the script is to automatically detect the column types from an input ``CSV``. This behaviour works as follows: