Add a straightforward index documentation and simplify quickstart

docs/index.md

@@ -3,19 +3,56 @@
 <!-- ================================================= -->
 
 # PyOrthanc
+**PyOrthanc** is a python client for the Orthanc REST API, which fully wraps all the methods of the REST API.
+Additionally, it provides many utility functions to interact with an Orthanc instance.
 
-Python library that wraps the Orthanc REST API and facilitates the manipulation of data with several cool utilities.
-What for ?
 
-The aim of the PyOrthanc module is to easy use the Orthanc Dicom server API.
+---
+Install PyOrthanc
+```bash
+pip install pyorthanc
+```
+---
+Then use the client:
+```python
+import pyorthanc
 
-It has access to the full available Orthanc API and get the useful return without dealing with http requests.
+client = pyorthanc.Orthanc('https://demo.orthanc-server.com')
+patient_ids = client.get_patients()
+```
+Interact with connected modalities
 
-It also allows you to find specifics series/studies/patients according to complex filters
+```python
+import pyorthanc
+
+modality = pyorthanc.Modality(client, 'MY_MODALITY')
+assert modality.echo()
+
+# C-Find on modality
+response = modality.query({'Level': 'Study', 'Query': {'PatientID': '*'}})
+
+# C-Move to target modality
+modality.move(response['ID'], {'TargetAet': 'target_modality'})
+```
+Find patients
+```python
+patients = pyorthanc.find_patients(client, {'PatientID': '*P001'})
+for patient in patients:
+    patient.labels
+    patient.is_stable
+    patient.name
+    ...
+    for study in patient.studies:
+        study.labels
+        study.date
+        ...
+        for series in study.series:
+            ...
+            for instance in series.instances:
+                pydicom_ds = instance.get_pydicom()
+```
 
 ## [First steps](tutorial/quickstart.md#first-steps)
-### [Requirements](tutorial/quickstart.md#requirements)
-### [Installation](tutorial/quickstart.md#installation)
 ### [Getting started](tutorial/quickstart.md#getting-started)
 * [Import pyorthanc library](tutorial/quickstart.md#import-pyorthanc-library)
 * [Connect to Orthanc](tutorial/quickstart.md#connect-to-orthanc)
@@ -25,14 +62,11 @@ It also allows you to find specifics series/studies/patients according to comple
 * [Query (C-Find) and Retrieve (C-Move) from remote modality:](tutorial/quickstart.md#query-c-find-and-retrieve-c-move-from-remote-modality)
 ### [Full basic examples](tutorial/quickstart.md#full-basic-examples)
 * [Access instance informations](tutorial/quickstart.md#access-instance-informations)
-### [Some useful commands](tutorial/quickstart.md#some-useful-commands)
-* [Docker commands](tutorial/quickstart.md#docker-commands)
 ### [Advanced examples](tutorial/advanced.md)
 * [Transfer data from a PACS to a Orthanc server](tutorial/advanced.md#transfer-data-from-a-pacs-to-a-orthanc-server)
 ### [Releases](releases/releases.md)
 * [Lastest release : 1.12.1](releases/releases.md#lastest-release-1121)
 * [Release 1.11.5](releases/releases.md#release-1115)
-## [Contribute](contributing.md#contribute)
 ## [Contacts](contacts.md#contacts)
 * [Maintainers Team](contacts.md#maintainers-team)
 * [Useful links](contacts.md#useful-links)

docs/tutorial/quickstart.md

@@ -1,68 +1,37 @@
 # First steps
 
-## Requirements
-
-- [x] Python3.8
-
 ## Installation
-
 ```bash
-python3 -m venv .venv
-source .venv/bin/activate
 pip install pyorthanc
 ```
 ## Getting started 
-### Import pyorthanc library
-```python
-import pyorthanc
-```
-
 ### Connect to Orthanc
 Here are some quick how to examples to use pyorthanc
 ```python
 from pyorthanc import Orthanc
 
-orthanc = Orthanc(url='http://localhost:8042/', 
-                  username='username', 
-                  password='password')
+orthanc = Orthanc(url='http://localhost:8042/', username='orthanc', password='orthanc')
 ```
 
 ### Upload DICOM files to Orthanc:
-
 ```python
-from pyorthanc import Orthanc
-
-orthanc = Orthanc(url='http://localhost:8042/', 
-                  username='username', 
-                  password='password')
-
 with open('A_DICOM_INSTANCE_PATH.dcm', 'rb') as file:
-   orthanc.post_instances(file.read())
+    orthanc.post_instances(file.read())
 ```
 ### Getting list of connected remote modalities:
 ```python
-from pyorthanc import Orthanc
-
-orthanc = Orthanc(url='http://localhost:8042/', 
-                  username='username', 
-                  password='password')
-
-orthanc.get_modalities()
+modalities = orthanc.get_modalities()
 ```
 
-
 ### Find and download patients according to criteria:
-
 ```python
-from pyorthanc import Orthanc, find_patients, retrieve_and_write_patients
-
-orthanc = Orthanc(url='https://demo.orthanc-server.com', username='', password='')
+from pyorthanc import find_patients, retrieve_and_write_patients
 
 patients = find_patients(
     client=orthanc,
     query={'PatientName': 'COMUNIX'} # Optional: filter with pyorthanc.Series object
 )
-retrieve_and_write_patients(patients, '.')
+retrieve_and_write_patients(patients, './patients_path')
 ```
 
 ### Query (C-Find) and Retrieve (C-Move) from remote modality:
@@ -87,54 +56,25 @@ modality.move(query_response['ID'], {'TargetAet': 'target_modality'})
 
 #### Anonymize patient:
 ```python
-from pyorthanc import Orthanc, Patient
-
-orthanc = Orthanc('http://localhost:8042', 'username', 'password')
+from pyorthanc import Patient
 
 patient_identifier = orthanc.get_patients()[0]
+patient = Patient(patient_identifier, orthanc)
 
-anonymized_patient = Patient(patient_identifier, orthanc).anonymize(
+anonymized_patient = patient.anonymize(
     keep=['PatientName'],   # You can keep/remove/replace the DICOM tags you want
     replace={'PatientID': 'TheNewPatientID'},
     remove=['ReferringPhysicianName'],
     force=True  # Needed when changing PatientID/StudyInstanceUID/SeriesInstanceUID/SOPInstanceUID
 )
-# Or directly with
-orthanc.post_patients_id_anonymize(patient_identifier)
-
-# result is: (you can retrieve DICOM file from ID)
-# {'ID': 'dd41f2f1-24838e1e-f01746fc-9715072f-189eb0a2',
-#  'Path': '/patients/dd41f2f1-24838e1e-f01746fc-9715072f-189eb0a2',
-#  'PatientID': 'dd41f2f1-24838e1e-f01746fc-9715072f-189eb0a2',
-#  'Type': 'Patient'}
 ```
 
 ## Full basic examples
 
 Be sure that Orthanc is running. The default URL (if running locally) is `http://localhost:8042`.
 
-Here is a list of examples to helps you getting started with pyorthanc
+Here is a list of examples to helps you getting started with pyorthanc.
 
-### Access instance informations
+### Access instance information
 
 [Get instance informations](https://github.com/ylemarechal/pyorthanc-examples/tree/main/basic/access_informations)
-
-## Some useful commands
-
-### Docker commands
-Start Orthanc
-```bash
-docker compose up -d
-```
-Stop Orthanc
-```bash
-docker compose stop
-```
-Restart Orthanc
-```bash
-docker compose restart
-```
-Delete Orthanc container
-```bash
-docker compose down
-```