Issue #630 and #635 DICOM and Orthanc.

Tidying up wording for DICOM page. Refs #630 [skip ci] docs only

Added section to prompt Conquest install in install-prep. Removed link to apache_on_windows that has been deleted. Refs #630 [skip ci] docs only

Note about conquest install, change start using it to refer to import docs. Refs #630 [skip ci] docs only

Moved import-from-file into new doc, intending to put Store and QR sections under import heading... Refs #630 [skip ci] docs only

Starting to move the conquest and DICOM store docs around. Refs #630 [skip ci] docs only

Forgot the link to the new document. Refs #630 [skip ci] docs only

Linking to the QR docs. Refs #630 [skip ci] docs only

Adding pages for bash/bat file creation for calling scripts from conquest. @dplatten - can you throw some content into conquest-scripts-windows.rst please? Refs #630 [skip ci] docs only

Organising the dicom.ini section. Refs #630 [skip ci] docs only

Spelling mistake in referencing dicom.ini example doc. Refs #630. [skip ci] docs only

More rearranging of the docs and content. Refs #630. [skip ci] docs only

Referenced the remaining existing conquest doc and removed the index reference to netdicom. Refs #630. [skip ci] docs only

Basic working lua script for importing RDSR objects to OpenREM when sent to Orthanc. Refs #635

Now drops any non SR/CT/MG/CR/DX modality objects, and processes what's left against the appropriate import script. Doesn't cater for Toshiba CT. Refs #635

Added stub for Toshiba, plus exiting function early if we won't be using it. Refs #635

Updated file so that it should work for Toshiba CT studies. Tested with test for Tosh CT removed on simple Dx study and works. Not tested the actual Toshiba import or the bit that removes the instances from Orthanc [skip ci]. References issue #635

Putting the delete instanceID back in [skip ci]. References issue #635

Corrected instance variable; made Philips import more explicit, as I think the Toshiba dose summary iamges are the same type [skip ci]. References issue 635

Renaming path to temp_fle_path and temp_files_path. Refs #635. [skip ci]

Missed one of the commented out references to path. Refs #635. [skip ci]

Removing the duplication of python path and python bin path. Refs #635. [skip ci]

Initial draft doc of Orthanc config. Doesn't cover installation and initial setup (that will be in different doc). Refs #635. [skip ci]

Correcting various errors and a few style changes. Refs #635. [skip ci]

Added stub to remind me to put something about permissions. Refs #635. [skip ci]

Added restart instructions for Windows [skip ci]. References issue 635

Amended Toshiba CT section so that it now works. Not fully tested yet. I can also confirm that this imports DR/DX correctly. I have changed the user-defined local variables as on my live system python.exe is in a different folder to the python scripts [skip ci]. References issue #635

Amended Toshiba CT section so that it creates a single folder rather than a nest of folders. This enables the Toshiba CT extractor to cleanly remove it once imported into OpenREM. I can confirm that this imports DR/DX, RDSR, Philips CT objects and older Toshiba CT data correctly. One of the issues I can see is that any non-Toshiba, non-Philips, non-RDSR CT data is currently deleted. Some of these can be imported with the Toshiba CT extractor [skip ci]. References issue #635

Amended Toshiba CT section so that it keeps physics studies. Also enabled Toshiba CT extractor for a range of CT systems that I know have worked with the extractor in the past. I think that the check for physics studies may fail if either the patient name or id are blank - need to check for nil in the script before using the values [skip ci]. References issue #635

Large changes to the file. The user can configure lists of manufacturer, model, station name, software version and serial numbers of systems to be ignored. This is useful to avoid importing things like computed radiography and specimen cabinet images into OpenREM. The user can now also configure a folder to keep physics test images in, and set a list of strings that are used in the patient name or id that indicate it is a physics test. There is also now a list of make/model pairs of CT scanners whose data can be successfully extracted with the Toshiba CT extractor [skip ci]. References issue #635

Correcting typo and removing superfluous variable [skip ci]. References issue #635

Addressed Ed's comments. Made these edits in PyCharm - trying to address all of its comments. These edits are untested. [skin ci]. Referenes issue #635

Initial attempt to revamp the docs for the current version of the Orthanc lua script. Refs #635, [skip ci]

Experimenting with other layouts. Refs #635, [skip ci]

Corrected link to raw version. Cut out some of the more obvious bus now you can see the original with comments. Need to do more along those lines, and increase the explanations. Also need to remove some of the examples that aren't useful for @dplatten, but might be useful elsewhere (eg Afga). Refs #635. [skip ci]

Changed syntax from table['x'] to table.x when accessing items in tables - I think it is tidier. I've also removed unused function parameters. These changes are untested. I wonder if we should enclose the OnStoredInstance code in an if origin['RequestOrigin'] ~= 'Lua' then block. This is used in an example to avoid infinite loops (http://book.orthanc-server.com/users/lua.html#important-remarks-about-auto-routing) [skip ci]. References issue #635

Missed a dot [skip ci]. References issue #635

Added zipping of physics studies - tested and working as expected on Windows with 7zip [skip ci]. References issue #635

Write details of any rejected DICOM instances to the Orthanc log file [skip ci]. References issue #635

Added some checks for nil Manufacturer and ManufacturerModelName tags; this has tripeed up my live Orthanc install (a Secondary Capture image of a contrast enhancement chart was the culprit) [skip ci]. References issue #635

Added in the extra settings (not yet referenced), changed the format of the customisation guide agin. Refs #635, [skip ci]

Corrected an earlier error (tried to delete instance rather than study). Physics images now only kept if element [1] of physics_to_keep is present. Toshiba CT extractor now only run if element [1][1] of toshiba_extractor_systems is present [skip ci]. References issue #635

Fixed syntax issue. Added nil value for physics and toshiba. Added link to toshiba resources. Refs #635, [skip ci]

Hopefully correcting link. Refs #635, [skip ci]

Added variables to enable/disable physics studies and Toshiba CT extractor sections. Changed a couple of variables to boolean where appropriate [skip ci]. References issue #635

Replaced the i and j key variables in several loops with a placeholder (_). Removes the final PyCharm criticisms of the code - I now have a green tick [skip ci]. References issue #635

Updated Windows service restart section, and included a Toshiba scanner in the tosh list. Documentation changes only [skip ci]. References issue #635

Spelling correction and additional comments to lua file. Updated docs. Refs #635, [skip ci]

Removing redundant {} instructions Updted permissions section. Refs #635, [skip ci]

Small change to remove duplication of the word 'linux'. Refs #635, [skip ci]

Promoted Orthanc in the DICOM Store section, added it to the installation prep doc. Refs #635, [skip ci]

Added quickstart to install prep. Refs #635, [skip ci]

Addded installation of OpenREM and pynetdicom to quickinstall. Refs #635, [skip ci]

Added some checks for nil when writing reject message to log. This failed due to a missing software versions tag in some CT images [skip ci]. References issue #635

Added virtualenvfolder to virtualenv locations to make it slightly clearer hopefully. Doesn't really ref #635, [skip ci]

Added further checks for nil before using tags. I think this covers all tag use in the script now [skip ci]. References issue #635

Missed a tag check [skip ci]. References issue #635

Added to zip command comment to make it clear that any switches required to create an archive must be included here [skip ci]. References issue #635

Clarified some parts of the DICOM store documentation. Tried to add a link to the section. Documentation changes only [skip ci]. References issue #635

Added virtualenvfolder to virtualenv locations to make it slightly clearer hopefully. Doesn't really ref #635, [skip ci]

Removed Store/QR further instructions from the install doc as it doesn't add anything. Refs #635, [skip ci]

Replaced references to now defunct netdicom page. Deleted file. Refs #635, [skip ci]

Remove propmt for adding linux example for Conquest. Not going to bother now we've added instructions for Orthanc. Refs #635, [skip ci]

Added bat file examples ffor Windoes with Conquest. Refs #635, [skip ci]

Minor edit to intro. Refs #630